lkball

Bindings for core::scoring::lkball namespace

class pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder

Bases: pybind11_builtins.pybind11_object

property B
property B_to_W
property B_to_W_norm
property B_to_W_norm2
property B_to_W_norm3
property Ot
property W
property W_to_Ot
property W_to_Ot_norm
property W_to_Ot_norm2
property W_to_Ot_norm3
colinear_dDome_dBase(self: pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder) pyrosetta.rosetta.numeric.xyzMatrix_double_t

C++: core::scoring::lkball::DerivativeFinder::colinear_dDome_dBase() –> class numeric::xyzMatrix<double>

colinear_dDome_dOther(self: pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder) pyrosetta.rosetta.numeric.xyzMatrix_double_t

C++: core::scoring::lkball::DerivativeFinder::colinear_dDome_dOther() –> class numeric::xyzMatrix<double>

colinear_dDome_dWater(self: pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder) pyrosetta.rosetta.numeric.xyzMatrix_double_t

C++: core::scoring::lkball::DerivativeFinder::colinear_dDome_dWater() –> class numeric::xyzMatrix<double>

property colinear_water
property cose
dDome_dBase(self: pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder) pyrosetta.rosetta.numeric.xyzMatrix_double_t

C++: core::scoring::lkball::DerivativeFinder::dDome_dBase() –> class numeric::xyzMatrix<double>

dDome_dOther(self: pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder) pyrosetta.rosetta.numeric.xyzMatrix_double_t

C++: core::scoring::lkball::DerivativeFinder::dDome_dOther() –> class numeric::xyzMatrix<double>

dDome_dWater(self: pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder) pyrosetta.rosetta.numeric.xyzMatrix_double_t

C++: core::scoring::lkball::DerivativeFinder::dDome_dWater() –> class numeric::xyzMatrix<double>

fringe_dDome_dBase(self: pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder) pyrosetta.rosetta.numeric.xyzMatrix_double_t

C++: core::scoring::lkball::DerivativeFinder::fringe_dDome_dBase() –> class numeric::xyzMatrix<double>

fringe_dDome_dOther(self: pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder) pyrosetta.rosetta.numeric.xyzMatrix_double_t

C++: core::scoring::lkball::DerivativeFinder::fringe_dDome_dOther() –> class numeric::xyzMatrix<double>

fringe_dDome_dWater(self: pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder) pyrosetta.rosetta.numeric.xyzMatrix_double_t

C++: core::scoring::lkball::DerivativeFinder::fringe_dDome_dWater() –> class numeric::xyzMatrix<double>

property norm_prod
property sine
property w_dist_
property wadj
property x
class pyrosetta.rosetta.core.scoring.lkball.DerivativeFinderWadj

Bases: pybind11_builtins.pybind11_object

property B
property B_to_W
property B_to_W_norm
property B_to_W_norm2
property B_to_W_norm3
property W
dWadj_dBase(self: pyrosetta.rosetta.core.scoring.lkball.DerivativeFinderWadj) pyrosetta.rosetta.numeric.xyzMatrix_double_t

C++: core::scoring::lkball::DerivativeFinderWadj::dWadj_dBase() –> class numeric::xyzMatrix<double>

dWadj_dWater(self: pyrosetta.rosetta.core.scoring.lkball.DerivativeFinderWadj) pyrosetta.rosetta.numeric.xyzMatrix_double_t

C++: core::scoring::lkball::DerivativeFinderWadj::dWadj_dWater() –> class numeric::xyzMatrix<double>

property w_dist_
property wadj
property x
class pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

%LKB_ResidueInfo holds the coordinates of the waters attached to a Residue

assign(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, src: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo

C++: core::scoring::lkball::LKB_ResidueInfo::operator=(const class core::scoring::lkball::LKB_ResidueInfo &) –> class core::scoring::lkball::LKB_ResidueInfo &

atom1_derivs(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t

C++: core::scoring::lkball::LKB_ResidueInfo::atom1_derivs() const –> const class utility::vector1<class numeric::xyzMatrix<double>, class std::allocator<class numeric::xyzMatrix<double> > > &

atom2_derivs(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t

C++: core::scoring::lkball::LKB_ResidueInfo::atom2_derivs() const –> const class utility::vector1<class numeric::xyzMatrix<double>, class std::allocator<class numeric::xyzMatrix<double> > > &

atom3_derivs(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t

C++: core::scoring::lkball::LKB_ResidueInfo::atom3_derivs() const –> const class utility::vector1<class numeric::xyzMatrix<double>, class std::allocator<class numeric::xyzMatrix<double> > > &

atom_weights(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) pyrosetta.rosetta.utility.vector1_utility_fixedsizearray1_double_2_t

C++: core::scoring::lkball::LKB_ResidueInfo::atom_weights() const –> const class utility::vector1<class utility::fixedsizearray1<double, 2>, class std::allocator<class utility::fixedsizearray1<double, 2> > > &

build_waters(*args, **kwargs)

Overloaded function.

  1. build_waters(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, rsd: pyrosetta.rosetta.core.conformation.Residue) -> None

  2. build_waters(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, rsd: pyrosetta.rosetta.core.conformation.Residue, compute_derivs: bool) -> None

C++: core::scoring::lkball::LKB_ResidueInfo::build_waters(const class core::conformation::Residue &, bool) –> void

clone(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) pyrosetta.rosetta.basic.datacache.CacheableData

C++: core::scoring::lkball::LKB_ResidueInfo::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>

has_waters(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) bool

C++: core::scoring::lkball::LKB_ResidueInfo::has_waters() const –> bool

initialize(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, rsd: pyrosetta.rosetta.core.chemical.ResidueType) None

C++: core::scoring::lkball::LKB_ResidueInfo::initialize(const class core::chemical::ResidueType &) –> void

matches_residue_type(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) bool

C++: core::scoring::lkball::LKB_ResidueInfo::matches_residue_type(const class core::chemical::ResidueType &) const –> bool

n_attached_waters(*args, **kwargs)

Overloaded function.

  1. n_attached_waters(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::scoring::lkball::LKB_ResidueInfo::n_attached_waters() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

  1. n_attached_waters(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, atom_index: int) -> int

C++: core::scoring::lkball::LKB_ResidueInfo::n_attached_waters(unsigned long) const –> unsigned long

residue_type(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) pyrosetta.rosetta.core.chemical.ResidueType

C++: core::scoring::lkball::LKB_ResidueInfo::residue_type() const –> const class core::chemical::ResidueType &

water_offset_for_atom(*args, **kwargs)

Overloaded function.

  1. water_offset_for_atom(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::scoring::lkball::LKB_ResidueInfo::water_offset_for_atom() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

  1. water_offset_for_atom(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, atom_index: int) -> int

C++: core::scoring::lkball::LKB_ResidueInfo::water_offset_for_atom(unsigned long) const –> unsigned long

waters(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: core::scoring::lkball::LKB_ResidueInfo::waters() const –> const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &

class pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

append(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo, rsd_info: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) None

C++: core::scoring::lkball::LKB_ResiduesInfo::append(class std::shared_ptr<class core::scoring::lkball::LKB_ResidueInfo>) –> void

assign(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo, : pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo) pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo

C++: core::scoring::lkball::LKB_ResiduesInfo::operator=(const class core::scoring::lkball::LKB_ResiduesInfo &) –> class core::scoring::lkball::LKB_ResiduesInfo &

clone(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo) pyrosetta.rosetta.basic.datacache.CacheableData

C++: core::scoring::lkball::LKB_ResiduesInfo::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>

size(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResiduesInfo) int

C++: core::scoring::lkball::LKB_ResiduesInfo::size() const –> unsigned long

class pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase

Bases: pyrosetta.rosetta.utility.SingletonBase_core_scoring_lkball_LKBallDatabase_t

A singleton class which stores data for LKBall terms. This is a separate singleton class, rather than static data on the LKB_ResidueInfo class so that the ResidueType destruction observer has a stable object to call back to.

static get_instance() core::scoring::lkball::LKBallDatabase

C++: utility::SingletonBase<core::scoring::lkball::LKBallDatabase>::get_instance() –> class core::scoring::lkball::LKBallDatabase *

get_water_builder_for_restype(self: pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype

C++: core::scoring::lkball::LKBallDatabase::get_water_builder_for_restype(const class core::chemical::ResidueType &) const –> class std::shared_ptr<const class core::scoring::lkball::WaterBuilderForRestype>

has(self: pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) bool

Returns true if the passed rsd_type is in the database

C++: core::scoring::lkball::LKBallDatabase::has(const class core::chemical::ResidueType &) const –> bool

initialize_residue_type(self: pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) None

C++: core::scoring::lkball::LKBallDatabase::initialize_residue_type(const class core::chemical::ResidueType &) –> void

reset_arrays_danger_expert_only(self: pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase) None

danger

C++: core::scoring::lkball::LKBallDatabase::reset_arrays_danger_expert_only() –> void

class pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo

Bases: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo

assign(self: pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo, src: pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo) pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo

C++: core::scoring::lkball::LKD_ResidueInfo::operator=(const class core::scoring::lkball::LKD_ResidueInfo &) –> class core::scoring::lkball::LKD_ResidueInfo &

atom1_derivs(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t

C++: core::scoring::lkball::LKB_ResidueInfo::atom1_derivs() const –> const class utility::vector1<class numeric::xyzMatrix<double>, class std::allocator<class numeric::xyzMatrix<double> > > &

atom2_derivs(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t

C++: core::scoring::lkball::LKB_ResidueInfo::atom2_derivs() const –> const class utility::vector1<class numeric::xyzMatrix<double>, class std::allocator<class numeric::xyzMatrix<double> > > &

atom3_derivs(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t

C++: core::scoring::lkball::LKB_ResidueInfo::atom3_derivs() const –> const class utility::vector1<class numeric::xyzMatrix<double>, class std::allocator<class numeric::xyzMatrix<double> > > &

atom_weights(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) pyrosetta.rosetta.utility.vector1_utility_fixedsizearray1_double_2_t

C++: core::scoring::lkball::LKB_ResidueInfo::atom_weights() const –> const class utility::vector1<class utility::fixedsizearray1<double, 2>, class std::allocator<class utility::fixedsizearray1<double, 2> > > &

build_waters(*args, **kwargs)

Overloaded function.

  1. build_waters(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, rsd: pyrosetta.rosetta.core.conformation.Residue) -> None

  2. build_waters(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, rsd: pyrosetta.rosetta.core.conformation.Residue, compute_derivs: bool) -> None

C++: core::scoring::lkball::LKB_ResidueInfo::build_waters(const class core::conformation::Residue &, bool) –> void

clear_occlusions(self: pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo) None

C++: core::scoring::lkball::LKD_ResidueInfo::clear_occlusions() –> void

clone(self: pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo) pyrosetta.rosetta.basic.datacache.CacheableData

C++: core::scoring::lkball::LKD_ResidueInfo::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>

has_waters(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) bool

C++: core::scoring::lkball::LKB_ResidueInfo::has_waters() const –> bool

initialize(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, rsd: pyrosetta.rosetta.core.chemical.ResidueType) None

C++: core::scoring::lkball::LKB_ResidueInfo::initialize(const class core::chemical::ResidueType &) –> void

matches_residue_type(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) bool

C++: core::scoring::lkball::LKB_ResidueInfo::matches_residue_type(const class core::chemical::ResidueType &) const –> bool

n_attached_waters(*args, **kwargs)

Overloaded function.

  1. n_attached_waters(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::scoring::lkball::LKB_ResidueInfo::n_attached_waters() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

  1. n_attached_waters(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, atom_index: int) -> int

C++: core::scoring::lkball::LKB_ResidueInfo::n_attached_waters(unsigned long) const –> unsigned long

residue_type(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) pyrosetta.rosetta.core.chemical.ResidueType

C++: core::scoring::lkball::LKB_ResidueInfo::residue_type() const –> const class core::chemical::ResidueType &

water_occlusions(self: pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo) pyrosetta.rosetta.utility.vector1_utility_fixedsizearray1_double_4_t

C++: core::scoring::lkball::LKD_ResidueInfo::water_occlusions() –> class utility::vector1<class utility::fixedsizearray1<double, 4>, class std::allocator<class utility::fixedsizearray1<double, 4> > > &

water_offset_for_atom(*args, **kwargs)

Overloaded function.

  1. water_offset_for_atom(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::scoring::lkball::LKB_ResidueInfo::water_offset_for_atom() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

  1. water_offset_for_atom(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, atom_index: int) -> int

C++: core::scoring::lkball::LKB_ResidueInfo::water_offset_for_atom(unsigned long) const –> unsigned long

water_sol_values(self: pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo) pyrosetta.rosetta.utility.vector1_double

C++: core::scoring::lkball::LKD_ResidueInfo::water_sol_values() const –> const class utility::vector1<double, class std::allocator<double> > &

waters(self: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo) pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: core::scoring::lkball::LKB_ResidueInfo::waters() const –> const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &

class pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy

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

accumulate_single_atom_contributions(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, atom1_n_attached_waters: int, atom1_water_offset: int, rsd1_waters: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, atom1_wts: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, atom2_type_index: int, atom2_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, lk_desolvation_of_atom1_by_atom2: float, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::lkball::LK_BallEnergy::accumulate_single_atom_contributions(unsigned long, unsigned long, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class utility::fixedsizearray1<double, 2> &, const class core::conformation::Residue &, const unsigned long, const class numeric::xyzVector<double> &, const double, class core::scoring::EMapVector &) const –> void

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

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

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) float

C++: core::scoring::lkball::LK_BallEnergy::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.lkball.LK_BallEnergy, : int, : pyrosetta.rosetta.core.conformation.Residue, : int, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::lkball::LK_BallEnergy::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

backbone_backbone_energy(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
The sum bbE(r1,r2) + bs(r1,r2) + bs(r2,r1) + ss(r1,r2) must equal rpe(r1,r2).

This function evaluates only the energies of bb/bb interactions.

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

backbone_sidechain_energy(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
The sum bbE(r1,r2) + bs(r1,r2) + bs(r2,r1) + ss(r1,r2) must equal rpe(r1,r2).

This function evaluates only the energies of bb/sc interactions; that is, the backbone from residue 1 with the sidechain of residue 2

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

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) None

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

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) None

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

calculate_lk_ball_atom_energies(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, atom1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atom1_n_attached_waters: int, atom1_water_offset: int, rsd1_waters: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, atom2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, lk_desolvation_of_atom1_by_atom2: float, lk_ball_desolvation_of_atom1_by_atom2: float) None

C++: core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies(const unsigned long, const class core::conformation::Residue &, unsigned long, unsigned long, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const unsigned long, const class core::conformation::Residue &, double &, double &) const –> void

calculate_lk_ball_atom_energies_cp(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, atom1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atom1_n_attached_waters: int, atom1_water_offset: int, atom1_waters: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, atom2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, cp_crossover: pyrosetta.rosetta.core.scoring.etable.count_pair.CPCrossoverBehavior, lk_desolvation_of_atom1_by_atom2: float, lk_ball_desolvation_of_atom1_by_atom2: float) None

C++: core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies_cp(const unsigned long, const class core::conformation::Residue &, unsigned long, unsigned long, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const unsigned long, const class core::conformation::Residue &, const enum core::scoring::etable::count_pair::CPCrossoverBehavior &, double &, double &) const –> void

calculate_lk_desolvation_of_single_atom_by_residue(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, atom1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) float

helper function for outside use

C++: core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(const unsigned long, const class core::conformation::Residue &, const class core::conformation::Residue &) –> double

calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, atom1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) float

C++: core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(const unsigned long, const class core::conformation::Residue &, const class core::conformation::Residue &) –> double

clone(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

clone

C++: core::scoring::lkball::LK_BallEnergy::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

defines_intrares_dof_derivatives(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, p: core::pose::Pose) bool
Use the dof_derivative interface for this energy method when

calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive.

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

defines_intrares_energy(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, : pyrosetta.rosetta.core.scoring.EMapVector) bool

C++: core::scoring::lkball::LK_BallEnergy::defines_intrares_energy(const class core::scoring::EMapVector &) const –> bool

defines_intrares_energy_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, res: pyrosetta.rosetta.core.conformation.Residue) bool
If a score function defines no intra-residue scores for a particular

residue, then it may opt-out of being asked during minimization to evaluate the score for this residue.

C++: core::scoring::methods::TwoBodyEnergy::defines_intrares_energy_for_residue(const class core::conformation::Residue &) const –> bool

defines_score_for_residue_pair(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, res_moving_wrt_eachother: bool) bool
During minimization, energy methods are allowed to decide that they say nothing

about a particular residue pair (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default implementation returns “true” for all residue pairs. Context-dependent two-body energies have the option of behaving as if they are context-independent by returning “false” for residue pairs that do no move wrt each other.

C++: core::scoring::methods::TwoBodyEnergy::defines_score_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, bool) const –> bool

divides_backbone_and_sidechain_energetics(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) bool
Let the energy-method consumers (e.g. the packer) use bounding-sphere logic for

deciding whether bb/bb, bb/sc, and sc/sc energies should be evaluated.

C++: core::scoring::lkball::LK_BallEnergy::divides_backbone_and_sidechain_energetics() const –> bool

etable(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) pyrosetta.rosetta.core.scoring.etable.Etable

C++: core::scoring::lkball::LK_BallEnergy::etable() const –> const class core::scoring::etable::Etable &

etable_bins_per_A2(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) float

C++: core::scoring::lkball::LK_BallEnergy::etable_bins_per_A2() const –> double

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) None

C++: core::scoring::lkball::LK_BallEnergy::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

eval_d_lk_fraction_dr_over_r(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, d2_delta: float, width: float) float

C++: core::scoring::lkball::LK_BallEnergy::eval_d_lk_fraction_dr_over_r(const double, const double) const –> double

eval_desolvation_derivs_no_count_pair(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, d2: float, atom1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atom2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, atom1_lk_desolvation_by_atom2_deriv: float, atom2_lk_desolvation_by_atom1_deriv: float) None

C++: core::scoring::lkball::LK_BallEnergy::eval_desolvation_derivs_no_count_pair(const double, const unsigned long, const class core::conformation::Residue &, const unsigned long, const class core::conformation::Residue &, double &, double &) –> void

eval_intrares_derivatives(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None
Evaluate the derivative for the intra-residue component of this energy method

for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.

C++: core::scoring::methods::TwoBodyEnergy::eval_intrares_derivatives(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::EMapVector &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

eval_intrares_energy(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.scoring.EMapVector) None

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

eval_intrares_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, data_cache: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) None
Evaluate the intra-residue energy for a given residue using the data held within the

ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return “true” in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

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

eval_intraresidue_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, dof_id: pyrosetta.rosetta.core.id.DOF_ID, torsion_id: core::id::TorsionID, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector) float
Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::TwoBodyEnergy::eval_intraresidue_dof_derivative(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::id::DOF_ID &, const class core::id::TorsionID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &) const –> double

eval_lk_fraction(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, d2_delta: float, width: float) float

C++: core::scoring::lkball::LK_BallEnergy::eval_lk_fraction(const double, const double) const –> double

eval_residue_pair_derivatives(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, : core::scoring::ResSingleMinimizationData, : core::scoring::ResSingleMinimizationData, min_data: core::scoring::ResPairMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, r1_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None

C++: core::scoring::lkball::LK_BallEnergy::eval_residue_pair_derivatives(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResPairMinimizationData &, const class core::pose::Pose &, const class core::scoring::EMapVector &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

evaluate_rotamer_background_energies(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, energy_vector: pyrosetta.rosetta.utility.vector1_float) None

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

evaluate_rotamer_background_energy_maps(self: pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, emaps: pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector) None
Batch computation of rotamer/background energies. Need not be overriden

in derived class – by default, iterates over all rotamers in the set, and calls derived class’s residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range

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

evaluate_rotamer_intrares_energies(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, energies: pyrosetta.rosetta.utility.vector1_float) None
Batch computation of rotamer intrares energies. Need not be overriden in

derived class – by default, iterates over all rotamers, and calls derived class’s intrares _energy method.

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

evaluate_rotamer_intrares_energy_maps(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emaps: pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector) None
Batch computation of rotamer intrares energy map. Need not be overriden in

derived class – by default, iterates over all rotamers, and calls derived class’s intrares _energy method.

C++: core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_intrares_energy_maps(const class core::conformation::RotamerSetBase &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, 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.lkball.LK_BallEnergy, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) None

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

fasol_max_dis2(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) float

C++: core::scoring::lkball::LK_BallEnergy::fasol_max_dis2() const –> double

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.core.scoring.lkball.LK_BallEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, totals: pyrosetta.rosetta.core.scoring.EMapVector) None

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

get_d2_low(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, idx: int) float

C++: core::scoring::lkball::LK_BallEnergy::get_d2_low(unsigned long) const –> double

get_lk_fractional_contribution(*args, **kwargs)

Overloaded function.

  1. get_lk_fractional_contribution(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, atom2_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, atom2_type_index: int, atom1_n_attached_waters: int, atom1_water_offset: int, rsd1_waters: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, d_weighted_d2_d_di: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, weighted_water_dis2: float) -> float

C++: core::scoring::lkball::LK_BallEnergy::get_lk_fractional_contribution(const class numeric::xyzVector<double> &, const unsigned long, unsigned long, unsigned long, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, class utility::fixedsizearray1<double, 4> &, double &) const –> double

  1. get_lk_fractional_contribution(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, atom2_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, atom2_type_index: int, atom1_n_attached_waters: int, atom1_water_offset: int, rsd1_waters: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) -> float

C++: core::scoring::lkball::LK_BallEnergy::get_lk_fractional_contribution(const class numeric::xyzVector<double> &, const unsigned long, const unsigned long, const unsigned long, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) const –> double

get_lk_fractional_contribution_for_single_water(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, atom2_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, atom2_type: int, atom1_water: pyrosetta.rosetta.numeric.xyzVector_double_t) float

C++: core::scoring::lkball::LK_BallEnergy::get_lk_fractional_contribution_for_single_water(const class numeric::xyzVector<double> &, const unsigned long, const class numeric::xyzVector<double> &) const –> double

get_lkbr_fractional_contribution(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, atom1_base: pyrosetta.rosetta.numeric.xyzVector_double_t, atom2_base: pyrosetta.rosetta.numeric.xyzVector_double_t, atom1_n_attached_waters: int, atom2_n_attached_waters: int, atom1_water_offset: int, atom2_water_offset: int, rsd1_waters: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, rsd2_waters: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) float

C++: core::scoring::lkball::LK_BallEnergy::get_lkbr_fractional_contribution(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, unsigned long, unsigned long, unsigned long, unsigned long, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) const –> double

get_lkbr_fractional_contribution_noangle(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, atom1_n_attached_waters: int, atom2_n_attached_waters: int, atom1_water_offset: int, atom2_water_offset: int, rsd1_waters: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, rsd2_waters: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) float

C++: core::scoring::lkball::LK_BallEnergy::get_lkbr_fractional_contribution_noangle(unsigned long, unsigned long, unsigned long, unsigned long, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) const –> double

get_lkbridge_angle_widthscale(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) float

C++: core::scoring::lkball::LK_BallEnergy::get_lkbridge_angle_widthscale() const –> double

get_multi_water_fade(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) float

C++: core::scoring::lkball::LK_BallEnergy::get_multi_water_fade() const –> double

get_overlap_gap2(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) float

C++: core::scoring::lkball::LK_BallEnergy::get_overlap_gap2() const –> double

get_overlap_target_len2(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) float

C++: core::scoring::lkball::LK_BallEnergy::get_overlap_target_len2() const –> double

get_overlap_width_A2(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) float

C++: core::scoring::lkball::LK_BallEnergy::get_overlap_width_A2() const –> double

get_ramp_width_A2(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) float

C++: core::scoring::lkball::LK_BallEnergy::get_ramp_width_A2() const –> double

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.lkball.LK_BallEnergy) bool

Has pairwise energies, but no single-atom ones.

C++: core::scoring::lkball::LK_BallEnergy::has_atomistic_pairwise_energies() const –> bool

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

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

lkb_max_dis(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) float

C++: core::scoring::lkball::LK_BallEnergy::lkb_max_dis() const –> double

lkb_max_dis2(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) float

C++: core::scoring::lkball::LK_BallEnergy::lkb_max_dis2() const –> double

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

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

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, : pyrosetta.rosetta.core.pose.Pose) bool

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, pose: pyrosetta.rosetta.core.pose.Pose, rotamer_set: pyrosetta.rosetta.core.conformation.RotamerSetBase) None

C++: core::scoring::lkball::LK_BallEnergy::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_derivatives_for_residue_opportunity(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, : pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::lkball::LK_BallEnergy::requires_a_setup_for_derivatives_for_residue_opportunity(const class core::pose::Pose &) const –> bool

requires_a_setup_for_derivatives_for_residue_pair_opportunity(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, pose: core::pose::Pose) bool
Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, pose: pyrosetta.rosetta.core.pose.Pose) bool

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

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

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

residue_pair_energy(*args, **kwargs)

Overloaded function.

  1. residue_pair_energy(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

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

  1. residue_pair_energy(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd1_info: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, rsd2: pyrosetta.rosetta.core.conformation.Residue, rsd2_info: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::lkball::LK_BallEnergy::residue_pair_energy(const class core::conformation::Residue &, const class core::scoring::lkball::LKB_ResidueInfo &, const class core::conformation::Residue &, const class core::scoring::lkball::LKB_ResidueInfo &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

residue_pair_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) None
Evaluate the two-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit().

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

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_d2_bounds(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) None

C++: core::scoring::lkball::LK_BallEnergy::setup_d2_bounds() –> void

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

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

setup_for_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) None

C++: core::scoring::lkball::LK_BallEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

setup_for_derivatives_for_residue_pair(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: core::scoring::ResSingleMinimizationData, minsingle_data2: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, data_cache: core::scoring::ResPairMinimizationData) None

Do any setup work necessary before evaluating the derivatives for this residue pair

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResPairMinimizationData &) 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_minimizing_for_residue(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_map: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, resdata: core::scoring::ResSingleMinimizationData) None

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

setup_for_minimizing_for_residue_pair(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_map: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, res1data: core::scoring::ResSingleMinimizationData, res2data: core::scoring::ResSingleMinimizationData, pairdata: core::scoring::ResPairMinimizationData) None

C++: core::scoring::lkball::LK_BallEnergy::setup_for_minimizing_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, class core::scoring::ResPairMinimizationData &) const –> void

setup_for_packing(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) None

C++: core::scoring::lkball::LK_BallEnergy::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.core.scoring.lkball.LK_BallEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

  1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

  2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

C++: core::scoring::lkball::LK_BallEnergy::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

setup_for_scoring_for_residue_pair(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: core::scoring::ResSingleMinimizationData, minsingle_data2: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, data_cache: core::scoring::ResPairMinimizationData) None
Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

C++: core::scoring::methods::TwoBodyEnergy::setup_for_scoring_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResPairMinimizationData &) 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

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
The sum bbE(r1,r2) + bs(r1,r2) + bs(r2,r1) + ss(r1,r2) must equal rpe(r1,r2).

This function evaluates only the energies of sc/sc interactions.

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

slim_etable(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) bool

C++: core::scoring::lkball::LK_BallEnergy::slim_etable() const –> bool

solv1(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

C++: core::scoring::lkball::LK_BallEnergy::solv1() const –> const class ObjexxFCL::FArray3D<double> &

solv2(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

C++: core::scoring::lkball::LK_BallEnergy::solv2() const –> const class ObjexxFCL::FArray3D<double> &

sum_deriv_contributions_for_heavyatom_pair(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, d2: float, heavyatom1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd1_info: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, heavyatom2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, rsd2_info: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, : pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, cp_weight: float, r1_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None

C++: core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair(const double, const unsigned long, const class core::conformation::Residue &, const class core::scoring::lkball::LKB_ResidueInfo &, const unsigned long, const class core::conformation::Residue &, const class core::scoring::lkball::LKB_ResidueInfo &, const class core::pose::Pose &, const class core::scoring::EMapVector &, const double, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

sum_deriv_contributions_for_heavyatom_pair_one_way(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, heavyatom1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd1_info: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, heavyatom2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, rsd2_info: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, weights: pyrosetta.rosetta.core.scoring.EMapVector, weight_factor: float, d2: float, r1_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None

C++: core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way(const unsigned long, const class core::conformation::Residue &, const class core::scoring::lkball::LKB_ResidueInfo &, const unsigned long, const class core::conformation::Residue &, const class core::scoring::lkball::LKB_ResidueInfo &, const class core::scoring::EMapVector &, const double, const double, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy, : pyrosetta.rosetta.core.pose.Pose, resid: int) None

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

use_extended_intrares_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy) bool
Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy

during minimization routines should return “true” when this function is invoked on them. This class provides a default “return false” implementation so that classes not desiring to take advantage of this alternate interface need to do nothing.

C++: core::scoring::methods::TwoBodyEnergy::use_extended_intrares_energy_interface() const –> bool

use_extended_residue_pair_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy) bool
Rely on the extended version of the residue_pair_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return ‘true’ from this function to use the extended interface. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::TwoBodyEnergy::use_extended_residue_pair_energy_interface() const –> bool

version(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy) int

C++: core::scoring::lkball::LK_BallEnergy::version() const –> unsigned long

class pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergyCreator

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

assign(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergyCreator, : pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergyCreator) pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergyCreator

C++: core::scoring::lkball::LK_BallEnergyCreator::operator=(const class core::scoring::lkball::LK_BallEnergyCreator &) –> class core::scoring::lkball::LK_BallEnergyCreator &

create_energy_method(self: pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new LK_BallEnergy

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

class pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy

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

accumulate_single_atom_contributions(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, atom1: int, : int, atom1_n_attached_waters: int, atom1_start_water: int, atom1_waters: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, atom1_occlusions: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, rsd1: pyrosetta.rosetta.core.conformation.Residue, atom2_type_index: int, atom2_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, lk_desolvation_of_atom1_by_water: float, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::lkball::LK_DomeEnergy::accumulate_single_atom_contributions(const unsigned long, const unsigned long, unsigned long, unsigned long, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class utility::fixedsizearray1<double, 4> &, const class core::conformation::Residue &, const unsigned long, const class numeric::xyzVector<double> &, const double, class core::scoring::EMapVector &) const –> void

assign(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, : pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy) pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy

C++: core::scoring::lkball::LK_DomeEnergy::operator=(const class core::scoring::lkball::LK_DomeEnergy &) –> class core::scoring::lkball::LK_DomeEnergy &

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy) float

C++: core::scoring::lkball::LK_DomeEnergy::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

backbone_backbone_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) None
Evaluate the interaction between the backbone of rsd1 and the

backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

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

backbone_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) None
Evaluate the interaction between the backbone of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

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

bump_energy_backbone(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) None

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

bump_energy_full(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::scoring::EMapVector) None

C++: core::scoring::methods::TwoBodyEnergy::bump_energy_full(const class core::conformation::Residue &, 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.core.scoring.lkball.LK_DomeEnergy) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

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

property debug_disable_count_pair_
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

defines_intrares_dof_derivatives(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, p: core::pose::Pose) bool
Use the dof_derivative interface for this energy method when

calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive.

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

defines_intrares_energy(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, weights: pyrosetta.rosetta.core.scoring.EMapVector) bool

C++: core::scoring::lkball::LK_DomeEnergy::defines_intrares_energy(const class core::scoring::EMapVector &) const –> bool

defines_intrares_energy_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, res: pyrosetta.rosetta.core.conformation.Residue) bool
If a score function defines no intra-residue scores for a particular

residue, then it may opt-out of being asked during minimization to evaluate the score for this residue.

C++: core::scoring::methods::TwoBodyEnergy::defines_intrares_energy_for_residue(const class core::conformation::Residue &) const –> bool

defines_score_for_residue_pair(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, res_moving_wrt_eachother: bool) bool

C++: core::scoring::lkball::LK_DomeEnergy::defines_score_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, bool) const –> bool

divides_backbone_and_sidechain_energetics(self: pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy) bool
A derived class should return true for this function if it implements its own

versions of the backbone_backbone_energy, backbone_sidechain_energy and sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own versions of these functions, then calling code may avoid calling it on pairs of residues that are “provably distant” based on a pair of bounding spheres for a sidechains and backbones and this method’s atomic_interaction_cutoff energy method.

C++: core::scoring::methods::ShortRangeTwoBodyEnergy::divides_backbone_and_sidechain_energetics() const –> bool

dlk_frac_sigmoid(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, distance: float) float

C++: core::scoring::lkball::LK_DomeEnergy::dlk_frac_sigmoid(double) const –> double

dmy_lk_fraction(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, distance: float) float

C++: core::scoring::lkball::LK_DomeEnergy::dmy_lk_fraction(double) const –> double

dome_water_dist2(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, base_atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, water: pyrosetta.rosetta.numeric.xyzVector_double_t, other_atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, water_atom_distance: float, wadj_water: pyrosetta.rosetta.numeric.xyzVector_double_t) float

C++: core::scoring::lkball::LK_DomeEnergy::dome_water_dist2(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double &, class numeric::xyzVector<double> &) const –> double

property dump_dome_bridge_waters_
property dump_dome_waters_
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

eval_d_lk_fraction_dr_over_r(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, d2_delta: float, width: float) float

C++: core::scoring::lkball::LK_DomeEnergy::eval_d_lk_fraction_dr_over_r(const double, const double) const –> double

eval_intrares_derivatives(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, weights: core::scoring::EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None
Evaluate the derivative for the intra-residue component of this energy method

for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd.

C++: core::scoring::methods::TwoBodyEnergy::eval_intrares_derivatives(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::EMapVector &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

eval_intrares_energy(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

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

eval_intrares_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, data_cache: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) None
Evaluate the intra-residue energy for a given residue using the data held within the

ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return “true” in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies.

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

eval_intraresidue_dof_derivative(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, dof_id: pyrosetta.rosetta.core.id.DOF_ID, torsion_id: core::id::TorsionID, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector) float
Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,

and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::TwoBodyEnergy::eval_intraresidue_dof_derivative(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::id::DOF_ID &, const class core::id::TorsionID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &) const –> double

eval_lk_fraction(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, d2_delta: float, width: float) float

C++: core::scoring::lkball::LK_DomeEnergy::eval_lk_fraction(const double, const double) const –> double

eval_residue_pair_derivatives(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, : core::scoring::ResSingleMinimizationData, : core::scoring::ResSingleMinimizationData, min_data: core::scoring::ResPairMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, r1_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None

C++: core::scoring::lkball::LK_DomeEnergy::eval_residue_pair_derivatives(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResPairMinimizationData &, const class core::pose::Pose &, const class core::scoring::EMapVector &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

evaluate_rotamer_background_energies(self: pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, energy_vector: pyrosetta.rosetta.utility.vector1_float) None
Batch computation of rotamer/background energies. Need not be overriden

in derived class – by default, iterates over all rotamers in the set, and calls derived class’s residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range

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

evaluate_rotamer_background_energy_maps(self: pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, emaps: pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector) None
Batch computation of rotamer/background energies. Need not be overriden

in derived class – by default, iterates over all rotamers in the set, and calls derived class’s residue_pair_energy method for each one against the background rotamer Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range

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

evaluate_rotamer_intrares_energies(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, energies: pyrosetta.rosetta.utility.vector1_float) None
Batch computation of rotamer intrares energies. Need not be overriden in

derived class – by default, iterates over all rotamers, and calls derived class’s intrares _energy method.

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

evaluate_rotamer_intrares_energy_maps(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emaps: pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector) None
Batch computation of rotamer intrares energy map. Need not be overriden in

derived class – by default, iterates over all rotamers, and calls derived class’s intrares _energy method.

C++: core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_intrares_energy_maps(const class core::conformation::RotamerSetBase &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, 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.methods.ShortRangeTwoBodyEnergy, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, weights: core::scoring::EMapVector, energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) None
Batch computation of rotamer pair energies. Need not be overriden in

derived class – by default, iterates over all pairs of rotamers, and calls derived class’s residue_pair_energy method. Since short range rotamer pairs may not need calculation, the default method looks at blocks of residue type pairs and only calls the residue_pair_energy method if the rotamer pairs are within range

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

fill_occlusions_1way(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd1_info: pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo, rsd2: pyrosetta.rosetta.core.conformation.Residue) None

C++: core::scoring::lkball::LK_DomeEnergy::fill_occlusions_1way(const class core::conformation::Residue &, class core::scoring::lkball::LKD_ResidueInfo &, const class core::conformation::Residue &) const –> void

fill_static_occlusions(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::lkball::LK_DomeEnergy::fill_static_occlusions(class core::pose::Pose &) 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.lkball.LK_DomeEnergy, pose: pyrosetta.rosetta.core.pose.Pose) None

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

finalize_total_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: core::scoring::EMapVector) None
called by the ScoreFunction at the end of energy evaluation.

The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

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

get_avail(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, occl: float) float

C++: core::scoring::lkball::LK_DomeEnergy::get_avail(double) const –> double

get_dome_water(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, base_atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, water: pyrosetta.rosetta.numeric.xyzVector_double_t, other_atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, water_atom_distance: float, wadj_water: pyrosetta.rosetta.numeric.xyzVector_double_t) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::lkball::LK_DomeEnergy::get_dome_water(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double &, class numeric::xyzVector<double> &) const –> class numeric::xyzVector<double>

get_lkb_bridge2_fractional_1way(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, n_atom1_waters: int, atom1_start_water: int, n_atom2_waters: int, atom2_start_water: int, atom1_waters: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, atom2_waters: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, atom1_occlusions: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t) float

C++: core::scoring::lkball::LK_DomeEnergy::get_lkb_bridge2_fractional_1way(unsigned long, unsigned long, unsigned long, unsigned long, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class utility::fixedsizearray1<double, 4> &) const –> double

get_lkd_bridge_fractional_1way(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, atom1_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, n_atom1_waters: int, atom1_start_water: int, n_atom2_waters: int, atom2_start_water: int, atom1_waters: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, atom2_waters: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, atom1_occlusions: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t) float

C++: core::scoring::lkball::LK_DomeEnergy::get_lkd_bridge_fractional_1way(const class numeric::xyzVector<double> &, unsigned long, unsigned long, unsigned long, unsigned long, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, const class utility::fixedsizearray1<double, 4> &) const –> double

get_lkd_frac_dome_dist(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, dw_dist: float, atom2_type: float) float

C++: core::scoring::lkball::LK_DomeEnergy::get_lkd_frac_dome_dist(double, double) const –> double

get_sol_value(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, at: pyrosetta.rosetta.core.chemical.AtomType, nattached_waters: int) float

C++: core::scoring::lkball::LK_DomeEnergy::get_sol_value(const class core::chemical::AtomType &, unsigned long) const –> double

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.core.scoring.lkball.LK_DomeEnergy, : pyrosetta.rosetta.utility.vector1_bool) None

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

lk_ball(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy) pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy

C++: core::scoring::lkball::LK_DomeEnergy::lk_ball() const –> class std::shared_ptr<const class core::scoring::lkball::LK_BallEnergy>

lk_frac_sigmoid(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, distance: float) float

C++: core::scoring::lkball::LK_DomeEnergy::lk_frac_sigmoid(double) const –> double

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

C++: core::scoring::methods::ContextDependentTwoBodyEnergy::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

my_lk_fraction(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, distance: float) float

C++: core::scoring::lkball::LK_DomeEnergy::my_lk_fraction(double) const –> double

my_setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) None

C++: core::scoring::lkball::LK_DomeEnergy::my_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

occlusion_max(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy) float

C++: core::scoring::lkball::LK_DomeEnergy::occlusion_max() const –> double

occlusion_min(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy) float

C++: core::scoring::lkball::LK_DomeEnergy::occlusion_min() const –> double

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_derivatives_for_residue_opportunity(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, : pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::lkball::LK_DomeEnergy::requires_a_setup_for_derivatives_for_residue_opportunity(const class core::pose::Pose &) const –> bool

requires_a_setup_for_derivatives_for_residue_pair_opportunity(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, pose: core::pose::Pose) bool
Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

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

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, : pyrosetta.rosetta.core.pose.Pose) bool

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

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

all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so.

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

residue_pair_energy(*args, **kwargs)

Overloaded function.

  1. residue_pair_energy(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

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

  1. residue_pair_energy(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd1_info: pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo, rsd2: pyrosetta.rosetta.core.conformation.Residue, rsd2_info: pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::lkball::LK_DomeEnergy::residue_pair_energy(const class core::conformation::Residue &, const class core::scoring::lkball::LKD_ResidueInfo &, const class core::conformation::Residue &, const class core::scoring::lkball::LKD_ResidueInfo &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

residue_pair_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResPairMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) None
Evaluate the two-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit().

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

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_d2_bounds(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy) None

C++: core::scoring::lkball::LK_DomeEnergy::setup_d2_bounds() –> void

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_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : core::scoring::ResSingleMinimizationData, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) None

C++: core::scoring::lkball::LK_DomeEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) const –> void

setup_for_derivatives_for_residue_pair(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: core::scoring::ResSingleMinimizationData, minsingle_data2: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, data_cache: core::scoring::ResPairMinimizationData) None

Do any setup work necessary before evaluating the derivatives for this residue pair

C++: core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResPairMinimizationData &) const –> void

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.kinematics.MinimizerMapBase) None

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

setup_for_minimizing_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, minmap: core::kinematics::MinimizerMapBase, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, res_data_cache: core::scoring::ResSingleMinimizationData) None
Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase.

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

setup_for_minimizing_for_residue_pair(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.kinematics.MinimizerMapBase, : core::scoring::ResSingleMinimizationData, : core::scoring::ResSingleMinimizationData, pair_data: core::scoring::ResPairMinimizationData) None

C++: core::scoring::lkball::LK_DomeEnergy::setup_for_minimizing_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, class core::scoring::ResPairMinimizationData &) const –> void

setup_for_packing(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) None

C++: core::scoring::lkball::LK_DomeEnergy::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.core.scoring.lkball.LK_DomeEnergy, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

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

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

  1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

  2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue (who is still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called) have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. This function is used for both intra-residue setup and pre-inter-residue setup

C++: core::scoring::methods::TwoBodyEnergy::setup_for_scoring_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &) const –> void

setup_for_scoring_for_residue_pair(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, minsingle_data1: core::scoring::ResSingleMinimizationData, minsingle_data2: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, data_cache: core::scoring::ResPairMinimizationData) None
Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

C++: core::scoring::methods::TwoBodyEnergy::setup_for_scoring_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResPairMinimizationData &) const –> void

setup_poly_params(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy) None

C++: core::scoring::lkball::LK_DomeEnergy::setup_poly_params() –> 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

sidechain_sidechain_energy(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) None
Evaluate the interaction between the sidechain of rsd1 and the

sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy.

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

single_water_atom_fractions(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, base_atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, water_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, other_atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, other_atom_type_index: int, lk_dome_iso_frac: float, lk_dome_frac: float) None

C++: core::scoring::lkball::LK_DomeEnergy::single_water_atom_fractions(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, unsigned long, double &, double &) const –> void

single_water_water_bridge2_fraction_1way(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, water_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, other_water_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) float

C++: core::scoring::lkball::LK_DomeEnergy::single_water_water_bridge2_fraction_1way(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) const –> double

single_water_water_fraction_1way(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, base_atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, water_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, other_water_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) float

C++: core::scoring::lkball::LK_DomeEnergy::single_water_water_fraction_1way(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) const –> double

sum_deriv_contributions_for_heavyatom_pair(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, d2: float, heavyatom1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd1_info: pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo, heavyatom2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, rsd2_info: pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo, : pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, cp_weight: float, r1_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None

C++: core::scoring::lkball::LK_DomeEnergy::sum_deriv_contributions_for_heavyatom_pair(const double, const unsigned long, const class core::conformation::Residue &, const class core::scoring::lkball::LKD_ResidueInfo &, const unsigned long, const class core::conformation::Residue &, const class core::scoring::lkball::LKD_ResidueInfo &, const class core::pose::Pose &, const class core::scoring::EMapVector &, const double, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

sum_deriv_contributions_for_heavyatom_pair_one_way(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, heavyatom1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd1_info: pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo, heavyatom2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, rsd2_info: pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo, weights: pyrosetta.rosetta.core.scoring.EMapVector, weight_factor: float, d2: float, r1_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_at_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) None

C++: core::scoring::lkball::LK_DomeEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way(const unsigned long, const class core::conformation::Residue &, const class core::scoring::lkball::LKD_ResidueInfo &, const unsigned long, const class core::conformation::Residue &, const class core::scoring::lkball::LKD_ResidueInfo &, const class core::scoring::EMapVector &, const double, const double, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

update_cached_lkb_resinfo(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, compute_derivs: bool, clear_occlusions: bool) None

C++: core::scoring::lkball::LK_DomeEnergy::update_cached_lkb_resinfo(const class core::conformation::Residue &, class basic::datacache::BasicDataCache &, bool, 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

use_extended_intrares_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy) bool
Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy

during minimization routines should return “true” when this function is invoked on them. This class provides a default “return false” implementation so that classes not desiring to take advantage of this alternate interface need to do nothing.

C++: core::scoring::methods::TwoBodyEnergy::use_extended_intrares_energy_interface() const –> bool

use_extended_residue_pair_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy) bool
Rely on the extended version of the residue_pair_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return ‘true’ from this function to use the extended interface. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::TwoBodyEnergy::use_extended_residue_pair_energy_interface() const –> bool

version(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy) int

C++: core::scoring::lkball::LK_DomeEnergy::version() const –> unsigned long

w_dist(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy) float

C++: core::scoring::lkball::LK_DomeEnergy::w_dist() const –> double

water_adjust(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy) float

C++: core::scoring::lkball::LK_DomeEnergy::water_adjust() const –> double

water_atom_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy) float

C++: core::scoring::lkball::LK_DomeEnergy::water_atom_interaction_cutoff() const –> double

water_atom_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy) float

C++: core::scoring::lkball::LK_DomeEnergy::water_atom_interaction_cutoff2() const –> double

water_water_bridge_cutoff2(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy) float

C++: core::scoring::lkball::LK_DomeEnergy::water_water_bridge_cutoff2() const –> double

class pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergyCreator

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

assign(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergyCreator, : pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergyCreator) pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergyCreator

C++: core::scoring::lkball::LK_DomeEnergyCreator::operator=(const class core::scoring::lkball::LK_DomeEnergyCreator &) –> class core::scoring::lkball::LK_DomeEnergyCreator &

create_energy_method(self: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new LK_DomeEnergy

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

class pyrosetta.rosetta.core.scoring.lkball.ScoredBridgingWater

Bases: pybind11_builtins.pybind11_object

property lkbr_score
property lkbr_uncpl_score
property position
class pyrosetta.rosetta.core.scoring.lkball.WaterBuilder

Bases: pybind11_builtins.pybind11_object

Stores the internal coordinates of an ideal water position

atom1(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilder) int

C++: core::scoring::lkball::WaterBuilder::atom1() const –> unsigned long

atom2(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilder) int

C++: core::scoring::lkball::WaterBuilder::atom2() const –> unsigned long

atom3(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilder) int

C++: core::scoring::lkball::WaterBuilder::atom3() const –> unsigned long

build(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilder, rsd: pyrosetta.rosetta.core.conformation.Residue) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::lkball::WaterBuilder::build(const class core::conformation::Residue &) const –> class numeric::xyzVector<double>

derivatives(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilder, rsd: pyrosetta.rosetta.core.conformation.Residue, dw_da1: pyrosetta.rosetta.numeric.xyzMatrix_double_t, dw_da2: pyrosetta.rosetta.numeric.xyzMatrix_double_t, dw_da3: pyrosetta.rosetta.numeric.xyzMatrix_double_t) None

C++: core::scoring::lkball::WaterBuilder::derivatives(const class core::conformation::Residue &, class numeric::xyzMatrix<double> &, class numeric::xyzMatrix<double> &, class numeric::xyzMatrix<double> &) const –> void

class pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype, : pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype) pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype

C++: core::scoring::lkball::WaterBuilderForRestype::operator=(const class core::scoring::lkball::WaterBuilderForRestype &) –> class core::scoring::lkball::WaterBuilderForRestype &

atom_weights(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype) pyrosetta.rosetta.utility.vector1_utility_fixedsizearray1_double_2_t

C++: core::scoring::lkball::WaterBuilderForRestype::atom_weights() const –> const class utility::vector1<class utility::fixedsizearray1<double, 2>, class std::allocator<class utility::fixedsizearray1<double, 2> > > &

builders(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype) pyrosetta.rosetta.utility.vector1_utility_vector1_core_scoring_lkball_WaterBuilder_std_allocator_core_scoring_lkball_WaterBuilder_t

C++: core::scoring::lkball::WaterBuilderForRestype::builders() const –> const class utility::vector1<class utility::vector1<class core::scoring::lkball::WaterBuilder, class std::allocator<class core::scoring::lkball::WaterBuilder> >, class std::allocator<class utility::vector1<class core::scoring::lkball::WaterBuilder, class std::allocator<class core::scoring::lkball::WaterBuilder> > > > &

n_waters(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype) int

C++: core::scoring::lkball::WaterBuilderForRestype::n_waters() const –> unsigned long

n_waters_for_atom(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype) pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::scoring::lkball::WaterBuilderForRestype::n_waters_for_atom() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

water_offset_for_atom(self: pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype) pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::scoring::lkball::WaterBuilderForRestype::water_offset_for_atom() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

pyrosetta.rosetta.core.scoring.lkball.evaluate_lk_dome_energy_for_atom_ranges(lk_dome: pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd1_info: pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo, rsd2: pyrosetta.rosetta.core.conformation.Residue, rsd2_info: pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, cpfxn: pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction, res1_start_atom: int, res1_end_atom: int, res2_start_atom: int, res2_end_atom: int, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::lkball::evaluate_lk_dome_energy_for_atom_ranges(const class core::scoring::lkball::LK_DomeEnergy &, const class core::conformation::Residue &, const class core::scoring::lkball::LKD_ResidueInfo &, const class core::conformation::Residue &, const class core::scoring::lkball::LKD_ResidueInfo &, const class core::scoring::ScoreFunction &, const class core::scoring::etable::count_pair::CountPairFunction &, const unsigned long, const unsigned long, const unsigned long, const unsigned long, class core::scoring::EMapVector &) –> void