scoring¶

methods

Bindings for protocols::scoring namespace

class pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck¶

Bases: 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.

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

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.

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

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

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

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.

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

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: 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(*args, **kwargs)¶

Overloaded function.

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

distance(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo) -> float

Get the distance cutoff for interface calculations

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

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: 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: 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: 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

atomistic_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno: int, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None¶

Evaluate the (one body) energy associated with a particular atom

This may be a “self” energy, or it may be the single atom contribution from a whole structure term. NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_energies()

This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.

C++: core::scoring::methods::EnergyMethod::atomistic_energy(unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

atomistic_pair_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None¶

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_pairwise_energies()

This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.

C++: core::scoring::methods::EnergyMethod::atomistic_pair_energy(unsigned long, const class core::conformation::Residue &, unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

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

has_atomistic_energies(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → bool¶

Does this EnergyMethod have a non-trivial implementation of the (one body) atomistic energy method?: Note that this may return false even if the score term theoretically could support atomistic energies. And even if this function returns true, it’s not necessarily the case that all atoms will get assigned an energy, or that the sum over all atoms (or atom pairs) will result in the same energy as the residue-level approach. The atomistic functions are intended for supplemental informational purposes only. The residue-level energies are the main interface for EnergyMethods.

C++: core::scoring::methods::EnergyMethod::has_atomistic_energies() const –> bool

has_atomistic_pairwise_energies(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → bool¶

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?: NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

C++: core::scoring::methods::EnergyMethod::has_atomistic_pairwise_energies() const –> bool

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:

setup_for_packing() is called for all energy methods
rotamers are built
setup_for_packing_with_rotsets() is called for all energy methods
prepare_rotamers_for_packing() is called for all energy methods
The energy methods are asked to score all rotamers and rotamer pairs
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: 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.

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>

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