geometric_solvation

Bindings for core::scoring::geometric_solvation namespace

class pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne

Bases: pybind11_object

acc_occ_type_has_data(self: pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne, atom_type_index: int) → bool

tells, for a given atom type, if there are pwSHO parameters for acceptor-occluding atoms having

that type

C++: core::scoring::geometric_solvation::DatabaseOccSolEne::acc_occ_type_has_data(unsigned long) const –> bool

acc_occ_type_mapping(self: pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne, atom_type_index: int) → int

maps each atom type to one for which there are pwSHO parameters when atoms of the new type are

evaluated as occluding solvent H-bonds to acceptors

C++: core::scoring::geometric_solvation::DatabaseOccSolEne::acc_occ_type_mapping(unsigned long) const –> unsigned long

acc_type_has_data(self: pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne, atom_type_index: int) → bool

tells, for a given atom type, if there are pwSHO parameters for acceptors having that atom type

C++: core::scoring::geometric_solvation::DatabaseOccSolEne::acc_type_has_data(unsigned long) const –> bool

acc_type_mapping(self: pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne, atom_type_index: int) → int

maps each atom type to one for which there are pwSHO parameters when atoms of the new type are

evaluated as acceptors

C++: core::scoring::geometric_solvation::DatabaseOccSolEne::acc_type_mapping(unsigned long) const –> unsigned long

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne) → float

C++: core::scoring::geometric_solvation::DatabaseOccSolEne::atomic_interaction_cutoff() const –> const double &

don_occ_type_has_data(self: pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne, atom_type_index: int) → bool

tells, for a given atom type, if there are pwSHO parameters for donor-occluding atoms having

that type

C++: core::scoring::geometric_solvation::DatabaseOccSolEne::don_occ_type_has_data(unsigned long) const –> bool

don_occ_type_mapping(self: pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne, atom_type_index: int) → int

maps each atom type to one for which there are pwSHO parameters when atoms of the new type are

evaluated as occluding solvent H-bonds to donors

C++: core::scoring::geometric_solvation::DatabaseOccSolEne::don_occ_type_mapping(unsigned long) const –> unsigned long

don_type_has_data(self: pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne, atom_type_index: int) → bool

tells, for a given atom type, if there are pwSHO parameters for donors having that atom type

C++: core::scoring::geometric_solvation::DatabaseOccSolEne::don_type_has_data(unsigned long) const –> bool

don_type_mapping(self: pyrosetta.rosetta.core.scoring.geometric_solvation.DatabaseOccSolEne, atom_type_index: int) → int

maps each atom type to one for which there are pwSHO parameters when atoms of the new type are

evaluated as donors

C++: core::scoring::geometric_solvation::DatabaseOccSolEne::don_type_mapping(unsigned long) const –> unsigned long

class pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator

Bases: pybind11_object

atom_is_heavy(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, rsd: pyrosetta.rosetta.core.conformation.Residue, atm: int) → bool

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::atom_is_heavy(const class core::conformation::Residue &, const unsigned long) const –> bool

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator) → float

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::atomic_interaction_cutoff() const –> double

defines_score_for_residue_pair(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, res_moving_wrt_eachother: bool) → bool

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

eval_atom_energy(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(const class core::id::AtomID &, const class core::pose::Pose &) const –> double

eval_intrares_derivatives(*args, **kwargs)

Overloaded function.

1. eval_intrares_derivatives(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, geom_sol_intra_weight: float, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) -> None

2. eval_intrares_derivatives(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, geom_sol_intra_weight: float, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, just_rna: bool) -> None

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &, const double &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &, const bool) const –> void

eval_intrares_energy(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::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_residue_pair_derivatives(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, ires: pyrosetta.rosetta.core.conformation.Residue, jres: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, geom_sol_weight: float, r1_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::scoring::ResPairMinimizationData &, const class core::pose::Pose &, 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

geometric_sol_one_way_bb_bb(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, polar_rsd: pyrosetta.rosetta.core.conformation.Residue, occ_rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::geometric_sol_one_way_bb_bb(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &) const –> double

geometric_sol_one_way_sc(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, polar_rsd: pyrosetta.rosetta.core.conformation.Residue, occ_rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::geometric_sol_one_way_sc(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &) const –> double

get_atom_atom_geometric_solvation_for_acceptor(*args, **kwargs)

Overloaded function.

1. get_atom_atom_geometric_solvation_for_acceptor(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, acc_atm: int, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, occ_atm: int, occ_rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, energy: float) -> None

2. get_atom_atom_geometric_solvation_for_acceptor(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, acc_atm: int, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, occ_atm: int, occ_rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, energy: float, update_deriv: bool) -> None

3. get_atom_atom_geometric_solvation_for_acceptor(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, acc_atm: int, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, occ_atm: int, occ_rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, energy: float, update_deriv: bool, deriv: pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs) -> None

4. get_atom_atom_geometric_solvation_for_acceptor(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, acc_atm: int, acc_rsd: pyrosetta.rosetta.core.conformation.Residue, occ_atm: int, occ_rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, energy: float, update_deriv: bool, deriv: pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs, hbe: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple) -> None

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(const unsigned long, const class core::conformation::Residue &, const unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, double &, const bool, struct core::scoring::hbonds::HBondDerivs &, class core::scoring::hbonds::HBEvalTuple &) const –> void

get_atom_atom_geometric_solvation_for_donor(*args, **kwargs)

Overloaded function.

1. get_atom_atom_geometric_solvation_for_donor(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, don_h_atm: int, don_rsd: pyrosetta.rosetta.core.conformation.Residue, occ_atm: int, occ_rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, energy: float) -> None

2. get_atom_atom_geometric_solvation_for_donor(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, don_h_atm: int, don_rsd: pyrosetta.rosetta.core.conformation.Residue, occ_atm: int, occ_rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, energy: float, update_deriv: bool) -> None

3. get_atom_atom_geometric_solvation_for_donor(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, don_h_atm: int, don_rsd: pyrosetta.rosetta.core.conformation.Residue, occ_atm: int, occ_rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, energy: float, update_deriv: bool, deriv: pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs) -> None

4. get_atom_atom_geometric_solvation_for_donor(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, don_h_atm: int, don_rsd: pyrosetta.rosetta.core.conformation.Residue, occ_atm: int, occ_rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, energy: float, update_deriv: bool, deriv: pyrosetta.rosetta.core.scoring.hbonds.HBondDerivs, hbe: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple) -> None

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(const unsigned long, const class core::conformation::Residue &, const unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, double &, const bool, struct core::scoring::hbonds::HBondDerivs &, class core::scoring::hbonds::HBEvalTuple &) const –> void

get_count_pair_function(*args, **kwargs)

Overloaded function.

1. get_count_pair_function(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, res1: int, res2: int, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_count_pair_function(const unsigned long, const unsigned long, const class core::pose::Pose &) const –> class std::shared_ptr<const class core::scoring::etable::count_pair::CountPairFunction>

2. get_count_pair_function(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) -> pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_count_pair_function(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> class std::shared_ptr<const class core::scoring::etable::count_pair::CountPairFunction>

get_intrares_countpair(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, res: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairFunction

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_intrares_countpair(const class core::conformation::Residue &) const –> class std::shared_ptr<const class core::scoring::etable::count_pair::CountPairFunction>

precalculate_bb_bb_energy_for_design(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::precalculate_bb_bb_energy_for_design(const class core::pose::Pose &) const –> double

res_res_geometric_sol_one_way(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, polar_rsd: pyrosetta.rosetta.core.conformation.Residue, occ_rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::res_res_geometric_sol_one_way(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &) const –> double

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

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::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

residue_pair_energy_ext(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, min_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::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 –> double

setup_for_minimizing_for_residue_pair(self: pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pair_data: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) → None

C++: core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::setup_for_minimizing_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, class core::scoring::ResPairMinimizationData &) const –> void

class pyrosetta.rosetta.core.scoring.geometric_solvation.OccFitParam

Bases: pybind11_object

Members:

OccFitParam_amp

OccFitParam_dist_mu

OccFitParam_twice_dist_sigma_sq

OccFitParam_cos_angle_mu

OccFitParam_twice_cos_angle_sigma_sq

OccFitParam_max_sq_dist

OccFitParam_min_cos_angle

OccFitParam_num_params

OccFitParam_amp = <OccFitParam.OccFitParam_amp: 1>

OccFitParam_cos_angle_mu = <OccFitParam.OccFitParam_cos_angle_mu: 4>

OccFitParam_dist_mu = <OccFitParam.OccFitParam_dist_mu: 2>

OccFitParam_max_sq_dist = <OccFitParam.OccFitParam_max_sq_dist: 6>

OccFitParam_min_cos_angle = <OccFitParam.OccFitParam_min_cos_angle: 7>

OccFitParam_num_params = <OccFitParam.OccFitParam_min_cos_angle: 7>

OccFitParam_twice_cos_angle_sigma_sq = <OccFitParam.OccFitParam_twice_cos_angle_sigma_sq: 5>

OccFitParam_twice_dist_sigma_sq = <OccFitParam.OccFitParam_twice_dist_sigma_sq: 3>

property name

property value