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core::scoring::methods Namespace Reference

Namespaces

 dfire
 

Classes

class  BBDepCartBondedParameters
 
class  BBIndepCartBondedParameters
 
class  CartBondedParameters
 
class  ContextDependentLRTwoBodyEnergy
 
class  ContextDependentOneBodyEnergy
 
class  ContextDependentTwoBodyEnergy
 
class  ContextIndependentLRTwoBodyEnergy
 
class  ContextIndependentOneBodyEnergy
 
class  ContextIndependentTwoBodyEnergy
 
class  EnergyMethod
 base class for the energy method hierarchy More...
 
class  EnergyMethodCreator
 The EnergyMethodCreator class's responsibilities are to create on demand a new EnergyMethod class, and to tell the ScoringManager singleton which ScoreTypes the EnergyMethod it creates is responsible for. The EnergyMethodCreator must register itself with the ScoringManager at load time (before main() begins) so that the ScoringManager is ready to start creating EnergyMethods by the time the first ScoreFunction requests one. More...
 
class  EnergyMethodOptions
 
class  EnergyMethodRegistrator
 This templated class will register an instance of an EnergyMethodCreator (class T) with the ScoringManager. It will ensure that no energy method creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
 
class  FreeDOF_Options
 
class  LongRangeTwoBodyEnergy
 
class  MMBondAngleEnergy
 
class  MMBondAngleEnergyCreator
 
class  MMBondLengthEnergy
 
class  MMBondLengthEnergyCreator
 
class  MMLJEnergyInter
 
class  MMLJEnergyInterCreator
 
class  MMLJEnergyIntra
 
class  MMLJEnergyIntraCreator
 
class  MMTorsionEnergy
 
class  MMTorsionEnergyCreator
 
class  NeighborListData
 
class  NMerPSSMEnergy
 
class  NMerPSSMEnergyCreator
 
class  NMerRefEnergy
 
class  NMerRefEnergyCreator
 
class  NMerSVMEnergy
 
class  NMerSVMEnergyCreator
 
class  OneBodyEnergy
 
class  PyEnergyMethodRegistrator
 This class will register an instance of an EnergyMethodCreator (class T) with the ScoringManager. It will ensure that no energy method creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
 
struct  ResidueAtomOverlaps
 
class  ShortRangeTwoBodyEnergy
 
class  TwoBodyEnergy
 
class  WholeStructureEnergy
 Base class for EnergyMethods which are meaningful only on entire structures, for example, the Radius of Gyration. These EnergyMethods do all of their work in the "finalize_total_energy" section of score function evaluation. More...
 

Typedefs

typedef
utility::pointer::weak_ptr
< CartBondedParameters
CartBondedParametersAP
 
typedef
utility::pointer::weak_ptr
< CartBondedParameters const > 
CartBondedParametersCAP
 
typedef
utility::pointer::shared_ptr
< CartBondedParameters
CartBondedParametersOP
 
typedef
utility::pointer::shared_ptr
< CartBondedParameters const > 
CartBondedParametersCOP
 
typedef
utility::pointer::shared_ptr
< ContextDependentLRTwoBodyEnergy
ContextDependentLRTwoBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< ContextDependentLRTwoBodyEnergy
const > 
ContextDependentLRTwoBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< ContextDependentOneBodyEnergy
ContextDependentOneBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< ContextDependentTwoBodyEnergy
ContextDependentTwoBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< ContextDependentTwoBodyEnergy
const > 
ContextDependentTwoBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< ContextIndependentLRTwoBodyEnergy
ContextIndependentLRTwoBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< ContextIndependentLRTwoBodyEnergy
const > 
ContextIndependentLRTwoBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< ContextIndependentOneBodyEnergy
ContextIndependentOneBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< ContextIndependentOneBodyEnergy
const > 
ContextIndependentOneBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< ContextIndependentTwoBodyEnergy
ContextIndependentTwoBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< ContextIndependentTwoBodyEnergy
const > 
ContextIndependentTwoBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< EnergyMethod
EnergyMethodOP
 
typedef
utility::pointer::shared_ptr
< EnergyMethod const > 
EnergyMethodCOP
 
typedef
utility::pointer::shared_ptr
< EnergyMethodCreator
EnergyMethodCreatorOP
 
typedef
utility::pointer::shared_ptr
< EnergyMethodCreator const > 
EnergyMethodCreatorCOP
 
typedef
utility::pointer::shared_ptr
< EnergyMethodOptions
EnergyMethodOptionsOP
 
typedef
utility::pointer::shared_ptr
< EnergyMethodOptions const > 
EnergyMethodOptionsCOP
 
typedef
utility::pointer::shared_ptr
< FreeDOF_Options
FreeDOF_OptionsOP
 
typedef
utility::pointer::shared_ptr
< FreeDOF_Options const > 
FreeDOF_OptionsCOP
 
typedef
utility::pointer::shared_ptr
< LongRangeTwoBodyEnergy
LongRangeTwoBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< LongRangeTwoBodyEnergy const > 
LongRangeTwoBodyEnergyCOP
 
typedef
utility::pointer::weak_ptr
< MMBondAngleEnergy
MMBondAngleEnergyAP
 
typedef
utility::pointer::weak_ptr
< MMBondAngleEnergy const > 
MMBondAngleEnergyCAP
 
typedef
utility::pointer::shared_ptr
< MMBondAngleEnergy
MMBondAngleEnergyOP
 
typedef
utility::pointer::shared_ptr
< MMBondAngleEnergy const > 
MMBondAngleEnergyCOP
 
typedef
utility::pointer::weak_ptr
< MMBondLengthEnergy
MMBondLengthEnergyAP
 
typedef
utility::pointer::weak_ptr
< MMBondLengthEnergy const > 
MMBondLengthEnergyCAP
 
typedef
utility::pointer::shared_ptr
< MMBondLengthEnergy
MMBondLengthEnergyOP
 
typedef
utility::pointer::shared_ptr
< MMBondLengthEnergy const > 
MMBondLengthEnergyCOP
 
typedef
utility::pointer::weak_ptr
< MMLJEnergyInter
MMLJEnergyInterAP
 
typedef
utility::pointer::weak_ptr
< MMLJEnergyInter const > 
MMLJEnergyInterCAP
 
typedef
utility::pointer::shared_ptr
< MMLJEnergyInter
MMLJEnergyInterOP
 
typedef
utility::pointer::shared_ptr
< MMLJEnergyInter const > 
MMLJEnergyInterCOP
 
typedef
utility::pointer::weak_ptr
< MMLJEnergyIntra
MMLJEnergyIntraAP
 
typedef
utility::pointer::weak_ptr
< MMLJEnergyIntra const > 
MMLJEnergyIntraCAP
 
typedef
utility::pointer::shared_ptr
< MMLJEnergyIntra
MMLJEnergyIntraOP
 
typedef
utility::pointer::shared_ptr
< MMLJEnergyIntra const > 
MMLJEnergyIntraCOP
 
typedef
utility::pointer::shared_ptr
< NeighborListData
NeighborListDataOP
 
typedef
utility::pointer::shared_ptr
< NeighborListData const > 
NeighborListDataCOP
 
typedef std::pair
< mm::mm_torsion_atom_quad,
core::Real
mm_torsion_atom_quad_angle_pair
 
using mmtaqap_iter = utility::vector1< mm_torsion_atom_quad_angle_pair >::const_iterator
 
typedef
utility::pointer::weak_ptr
< MMTorsionEnergy
MMTorsionEnergyAP
 
typedef
utility::pointer::weak_ptr
< MMTorsionEnergy const > 
MMTorsionEnergyCAP
 
typedef
utility::pointer::shared_ptr
< MMTorsionEnergy
MMTorsionEnergyOP
 
typedef
utility::pointer::shared_ptr
< MMTorsionEnergy const > 
MMTorsionEnergyCOP
 
typedef
utility::pointer::shared_ptr
< OneBodyEnergy
OneBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< OneBodyEnergy const > 
OneBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< ShortRangeTwoBodyEnergy
ShortRangeTwoBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< ShortRangeTwoBodyEnergy
const > 
ShortRangeTwoBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< TwoBodyEnergy
TwoBodyEnergyOP
 
typedef
utility::pointer::shared_ptr
< TwoBodyEnergy const > 
TwoBodyEnergyCOP
 
typedef
utility::pointer::shared_ptr
< WholeStructureEnergy
WholeStructureEnergyOP
 
typedef
utility::pointer::shared_ptr
< NMerPSSMEnergy
NMerPSSMEnergyOP
 
typedef
utility::pointer::shared_ptr
< NMerPSSMEnergy const > 
NMerPSSMEnergyCOP
 
typedef
utility::pointer::shared_ptr
< NMerRefEnergy
NMerRefEnergyOP
 
typedef
utility::pointer::shared_ptr
< NMerRefEnergy const > 
NMerRefEnergyCOP
 
typedef
utility::pointer::shared_ptr
< NMerSVMEnergy
NMerSVMEnergyOP
 
typedef
utility::pointer::shared_ptr
< NMerSVMEnergy const > 
NMerSVMEnergyCOP
 

Enumerations

enum  EnergyMethodType {
  ci_2b = 1, cd_2b, ci_lr_2b, cd_lr_2b,
  ci_1b, cd_1b, ws, n_energy_method_types = ws
}
 
enum  EnergyMethods {
  etable_method = 1, dunbrack_method, hbond_method, elec_method,
  lkball_method, mm_lj_energy_inter_method, pair_e_method, reference_e_method,
  vdw_method, ramachandran_method, n_energy_methods = ramachandran_method
}
 
enum  LongRangeEnergyType {
  constraints_lr = 1, gen_born_lr, multipole_elec_lr, vdw_tinker_lr,
  sasa_lr, epr_deer_lr, PB_elec_lr, cart_bonded_lr,
  dna_dihedral_lr, gen_bonded_lr, rama2b_lr, ramaprepro_lr,
  aspartimide_penalty_lr, rna_suite_lr, tna_suite_lr, rna_stub_coord_lr,
  DFIRE, sym_bonus_lr, elec_dens_energy, elec_dens_fast_energy,
  elec_dens_cen_energy, elec_dens_allatom_cen_energy, elec_dens_atomwise_energy, patterson_corr_energy,
  fa_disulfide_energy, disulfide_matching_energy, centroid_disulfide_energy, n_long_range_types = centroid_disulfide_energy
}
 

Functions

void find_relevant_connections_onersd (pose::Pose const &pose, Size const seqpos, ResidueAtomOverlaps &branch_connection)
 
void find_relevant_connections (pose::Pose const &pose, utility::vector1< ResidueAtomOverlaps > &branch_connections)
 
bool is_lower_cutpoint (core::Size residue, core::pose::Pose const &pose)
 
bool is_upper_cutpoint (core::Size residue, core::pose::Pose const &pose)
 
void find_cutpoint_variants (core::pose::Pose const &pose, core::kinematics::FoldTree const &, utility::vector1< int > &cutpoints)
 
bool lower_upper_connected_across_cutpoint (core::conformation::Residue const &lower_rsd, core::conformation::Residue const &upper_rsd)
 Helper function for looking at residue connections to get lower/upper partners. More...
 
Size get_upper_cutpoint_partner_for_lower (core::pose::Pose const &pose, core::Size const lower_res)
 Instead of assuming cutpoint partner is simply cutpoint+1, find which residue connects via lower/upper. More...
 
Size get_lower_cutpoint_partner_for_upper (core::pose::Pose const &pose, core::Size const upper_res)
 Instead of assuming cutpoint partner is simply res-1, find which residue connects via lower/upper. More...
 
bool operator== (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
 used inside ScoreFunctionInfo::operator== More...
 
bool operator!= (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
 used inside ScoreFunctionInfo::operator== More...
 
std::ostream & operator<< (std::ostream &out, EnergyMethodOptions const &options)
 
bool operator== (FreeDOF_Options const &a, FreeDOF_Options const &b)
 
std::ostream & operator<< (std::ostream &out, const FreeDOF_Options &options)
 
static basic::Tracer TR ("core.mm.MMBondAngleEnergy")
 
static basic::Tracer TR ("core.mm.MMBondLengthEnergy")
 
static basic::Tracer TR ("core.scoring.methods.MMTorsionEnergy")
 
static basic::Tracer TR ("core.scoring.methods.OneBodyEnergy")
 
static basic::Tracer TR ("core.scoring.methods.TwoBodyEnergy")
 
static basic::Tracer tr ("core.scoring.methods")
 
core::Real get_residue_weight_by_ss (const char ss)
 
bool residues_interact (conformation::Residue const &rsd1, conformation::Residue const &rsd2, core::Real const interaction_cutoff)
 
bool atoms_interact (conformation::Residue const &rsd1, conformation::Residue const &rsd2, core::id::AtomID const &id1, core::id::AtomID const &id2, core::Real const interaction_cutoff)
 
void determine_lo_and_hi_residues (core::pose::Pose const &pose, core::Size const rsd1, core::Size const rsd2, bool &res1_is_lo, bool &res2_is_lo)
 Given two residues that may or may not be connected, determine which of the two, if any, is the lower one and which is the upper. More...
 
void create_long_range_energy_container (core::pose::Pose &pose, core::scoring::ScoreType const scoretype, core::scoring::methods::LongRangeEnergyType const lr_type)
 Determines whether a long-range energies container exists in the pose energies object. If not, creates a new one and appends the score type to it, if necessary. More...
 

Typedef Documentation

typedef utility::pointer::weak_ptr< CartBondedParameters const > core::scoring::methods::CartBondedParametersCAP
typedef utility::pointer::shared_ptr< CartBondedParameters const > core::scoring::methods::CartBondedParametersCOP
typedef utility::pointer::shared_ptr< EnergyMethod const > core::scoring::methods::EnergyMethodCOP
typedef utility::pointer::shared_ptr< EnergyMethodCreator const > core::scoring::methods::EnergyMethodCreatorCOP
typedef utility::pointer::shared_ptr< EnergyMethodCreator > core::scoring::methods::EnergyMethodCreatorOP
typedef utility::pointer::shared_ptr< EnergyMethod > core::scoring::methods::EnergyMethodOP
typedef utility::pointer::shared_ptr< EnergyMethodOptions const > core::scoring::methods::EnergyMethodOptionsCOP
typedef utility::pointer::shared_ptr< EnergyMethodOptions > core::scoring::methods::EnergyMethodOptionsOP
typedef utility::pointer::shared_ptr< FreeDOF_Options const > core::scoring::methods::FreeDOF_OptionsCOP
typedef utility::pointer::shared_ptr< FreeDOF_Options > core::scoring::methods::FreeDOF_OptionsOP
typedef utility::pointer::shared_ptr< LongRangeTwoBodyEnergy const > core::scoring::methods::LongRangeTwoBodyEnergyCOP
typedef utility::pointer::weak_ptr< MMBondAngleEnergy > core::scoring::methods::MMBondAngleEnergyAP
typedef utility::pointer::weak_ptr< MMBondAngleEnergy const > core::scoring::methods::MMBondAngleEnergyCAP
typedef utility::pointer::shared_ptr< MMBondAngleEnergy const > core::scoring::methods::MMBondAngleEnergyCOP
typedef utility::pointer::shared_ptr< MMBondAngleEnergy > core::scoring::methods::MMBondAngleEnergyOP
typedef utility::pointer::weak_ptr< MMBondLengthEnergy const > core::scoring::methods::MMBondLengthEnergyCAP
typedef utility::pointer::shared_ptr< MMBondLengthEnergy const > core::scoring::methods::MMBondLengthEnergyCOP
typedef utility::pointer::shared_ptr< MMBondLengthEnergy > core::scoring::methods::MMBondLengthEnergyOP
typedef utility::pointer::weak_ptr< MMLJEnergyInter > core::scoring::methods::MMLJEnergyInterAP
typedef utility::pointer::weak_ptr< MMLJEnergyInter const > core::scoring::methods::MMLJEnergyInterCAP
typedef utility::pointer::shared_ptr< MMLJEnergyInter const > core::scoring::methods::MMLJEnergyInterCOP
typedef utility::pointer::shared_ptr< MMLJEnergyInter > core::scoring::methods::MMLJEnergyInterOP
typedef utility::pointer::weak_ptr< MMLJEnergyIntra > core::scoring::methods::MMLJEnergyIntraAP
typedef utility::pointer::weak_ptr< MMLJEnergyIntra const > core::scoring::methods::MMLJEnergyIntraCAP
typedef utility::pointer::shared_ptr< MMLJEnergyIntra const > core::scoring::methods::MMLJEnergyIntraCOP
typedef utility::pointer::shared_ptr< MMLJEnergyIntra > core::scoring::methods::MMLJEnergyIntraOP
using core::scoring::methods::mmtaqap_iter = typedef utility::vector1<mm_torsion_atom_quad_angle_pair>::const_iterator
typedef utility::pointer::weak_ptr< MMTorsionEnergy > core::scoring::methods::MMTorsionEnergyAP
typedef utility::pointer::weak_ptr< MMTorsionEnergy const > core::scoring::methods::MMTorsionEnergyCAP
typedef utility::pointer::shared_ptr< MMTorsionEnergy const > core::scoring::methods::MMTorsionEnergyCOP
typedef utility::pointer::shared_ptr< MMTorsionEnergy > core::scoring::methods::MMTorsionEnergyOP
typedef utility::pointer::shared_ptr< NeighborListData const > core::scoring::methods::NeighborListDataCOP
typedef utility::pointer::shared_ptr< NeighborListData > core::scoring::methods::NeighborListDataOP
typedef utility::pointer::shared_ptr< NMerPSSMEnergy const > core::scoring::methods::NMerPSSMEnergyCOP
typedef utility::pointer::shared_ptr< NMerPSSMEnergy > core::scoring::methods::NMerPSSMEnergyOP
typedef utility::pointer::shared_ptr< NMerRefEnergy const > core::scoring::methods::NMerRefEnergyCOP
typedef utility::pointer::shared_ptr< NMerRefEnergy > core::scoring::methods::NMerRefEnergyOP
typedef utility::pointer::shared_ptr< NMerSVMEnergy const > core::scoring::methods::NMerSVMEnergyCOP
typedef utility::pointer::shared_ptr< NMerSVMEnergy > core::scoring::methods::NMerSVMEnergyOP
typedef utility::pointer::shared_ptr< OneBodyEnergy const > core::scoring::methods::OneBodyEnergyCOP
typedef utility::pointer::shared_ptr< OneBodyEnergy > core::scoring::methods::OneBodyEnergyOP
typedef utility::pointer::shared_ptr< ShortRangeTwoBodyEnergy const > core::scoring::methods::ShortRangeTwoBodyEnergyCOP
typedef utility::pointer::shared_ptr< TwoBodyEnergy const > core::scoring::methods::TwoBodyEnergyCOP
typedef utility::pointer::shared_ptr< TwoBodyEnergy > core::scoring::methods::TwoBodyEnergyOP

Enumeration Type Documentation

Enumerator
etable_method 
dunbrack_method 
hbond_method 
elec_method 
lkball_method 
mm_lj_energy_inter_method 
pair_e_method 
reference_e_method 
vdw_method 
ramachandran_method 
n_energy_methods 
Enumerator
ci_2b 
cd_2b 
ci_lr_2b 
cd_lr_2b 
ci_1b 
cd_1b 
ws 
n_energy_method_types 
Enumerator
constraints_lr 
gen_born_lr 
multipole_elec_lr 
vdw_tinker_lr 
sasa_lr 
epr_deer_lr 
PB_elec_lr 
cart_bonded_lr 
dna_dihedral_lr 
gen_bonded_lr 
rama2b_lr 
ramaprepro_lr 
aspartimide_penalty_lr 
rna_suite_lr 
tna_suite_lr 
rna_stub_coord_lr 
DFIRE 
sym_bonus_lr 
elec_dens_energy 
elec_dens_fast_energy 
elec_dens_cen_energy 
elec_dens_allatom_cen_energy 
elec_dens_atomwise_energy 
patterson_corr_energy 
fa_disulfide_energy 
disulfide_matching_energy 
centroid_disulfide_energy 
n_long_range_types 

Function Documentation

bool core::scoring::methods::atoms_interact ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
core::id::AtomID const &  id1,
core::id::AtomID const &  id2,
core::Real const  interaction_cutoff 
)
void core::scoring::methods::create_long_range_energy_container ( core::pose::Pose pose,
core::scoring::ScoreType const  scoretype,
core::scoring::methods::LongRangeEnergyType const  lr_type 
)

Determines whether a long-range energies container exists in the pose energies object. If not, creates a new one and appends the score type to it, if necessary.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::pose::Pose::energies().

Referenced by core::energy_methods::RamaPreProEnergy::setup_for_scoring(), and core::energy_methods::AspartimidePenaltyEnergy::setup_for_scoring().

void core::scoring::methods::determine_lo_and_hi_residues ( core::pose::Pose const &  pose,
core::Size const  rsd1,
core::Size const  rsd2,
bool res1_is_lo,
bool res2_is_lo 
)

Given two residues that may or may not be connected, determine which of the two, if any, is the lower one and which is the upper.

Inputs are rsd1 and rsd2; outputs are rsd1_is_lo and rsd2_is_lo. Both will be false if the residues aren't connected (s.t. the C of one connected to some connection of the other).

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::conformation::Residue::has_upper_connect(), core::chemical::ResidueConnection::index(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), and core::conformation::Residue::upper_connect().

Referenced by core::energy_methods::RamaPreProEnergy::defines_residue_pair_energy(), core::energy_methods::AspartimidePenaltyEnergy::defines_residue_pair_energy(), core::energy_methods::RamaPreProEnergy::residue_pair_energy(), and core::energy_methods::AspartimidePenaltyEnergy::residue_pair_energy().

void core::scoring::methods::find_cutpoint_variants ( core::pose::Pose const &  pose,
core::kinematics::FoldTree const &  ,
utility::vector1< int > &  cutpoints 
)
void core::scoring::methods::find_relevant_connections ( pose::Pose const &  pose,
utility::vector1< ResidueAtomOverlaps > &  branch_connections 
)
void core::scoring::methods::find_relevant_connections_onersd ( pose::Pose const &  pose,
Size const  seqpos,
ResidueAtomOverlaps &  branch_connection 
)
core::Size core::scoring::methods::get_lower_cutpoint_partner_for_upper ( pose::Pose const &  pose,
Size const  upper_res 
)
core::Real core::scoring::methods::get_residue_weight_by_ss ( const char  ss)
core::Size core::scoring::methods::get_upper_cutpoint_partner_for_lower ( pose::Pose const &  pose,
Size const  lower_res 
)
bool core::scoring::methods::is_lower_cutpoint ( core::Size  residue,
core::pose::Pose const &  pose 
)
bool core::scoring::methods::is_upper_cutpoint ( core::Size  residue,
core::pose::Pose const &  pose 
)
bool core::scoring::methods::lower_upper_connected_across_cutpoint ( core::conformation::Residue const &  lower_rsd,
core::conformation::Residue const &  upper_rsd 
)
bool core::scoring::methods::operator!= ( EnergyMethodOptions const &  a,
EnergyMethodOptions const &  b 
)
std::ostream& core::scoring::methods::operator<< ( std::ostream &  out,
const FreeDOF_Options &  options 
)
std::ostream & core::scoring::methods::operator<< ( std::ostream &  out,
EnergyMethodOptions const &  options 
)
bool core::scoring::methods::operator== ( FreeDOF_Options const &  a,
FreeDOF_Options const &  b 
)
bool core::scoring::methods::operator== ( EnergyMethodOptions const &  a,
EnergyMethodOptions const &  b 
)

used inside ScoreFunctionInfo::operator==

References core::scoring::methods::EnergyMethodOptions::aa_composition_setup_files_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_assume_const_backbone_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_burial_atomic_depth_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_burial_probe_radius_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_burial_resolution_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_hbond_bonus_cross_chain_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_hbond_energy_threshold_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_natural_corrections1_, core::scoring::methods::EnergyMethodOptions::approximate_buried_unsat_penalty_oversat_penalty_, core::scoring::methods::EnergyMethodOptions::arg_cation_pi_his_can_be_pi_, core::scoring::methods::EnergyMethodOptions::aspartimide_penalty_value_, core::scoring::methods::EnergyMethodOptions::atom_vdw_atom_type_set_name_, core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score_, core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set_, core::scoring::methods::EnergyMethodOptions::cartbonded_ang_, core::scoring::methods::EnergyMethodOptions::cartbonded_improper_, core::scoring::methods::EnergyMethodOptions::cartbonded_len_, core::scoring::methods::EnergyMethodOptions::cartbonded_linear_, core::scoring::methods::EnergyMethodOptions::cartbonded_proton_, core::scoring::methods::EnergyMethodOptions::cartbonded_skip_cutpoints_, core::scoring::methods::EnergyMethodOptions::cartbonded_tors_, core::scoring::methods::EnergyMethodOptions::count_pair_full_, core::scoring::methods::EnergyMethodOptions::count_pair_hybrid_, core::scoring::methods::EnergyMethodOptions::covalent_labeling_fa_input_, core::scoring::methods::EnergyMethodOptions::covalent_labeling_input_, core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep_, core::scoring::methods::EnergyMethodOptions::dump_trajectory_gz_, core::scoring::methods::EnergyMethodOptions::dump_trajectory_prefix_, core::scoring::methods::EnergyMethodOptions::dump_trajectory_stride_, core::scoring::methods::EnergyMethodOptions::elec_die_, core::scoring::methods::EnergyMethodOptions::elec_group_file_, core::scoring::methods::EnergyMethodOptions::elec_max_dis_, core::scoring::methods::EnergyMethodOptions::elec_min_dis_, core::scoring::methods::EnergyMethodOptions::elec_no_dis_dep_die_, core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_D0_, core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_D_, core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_die_, core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_S_, core::scoring::methods::EnergyMethodOptions::envsmooth_zero_negatives_, core::scoring::methods::EnergyMethodOptions::etable_options_, core::scoring::methods::EnergyMethodOptions::eval_intrares_elec_ST_only_, core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA_, core::scoring::methods::EnergyMethodOptions::exclude_intra_res_protein_, core::scoring::methods::EnergyMethodOptions::exclude_monomer_fa_elec_, core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_elec_, core::scoring::methods::EnergyMethodOptions::exclude_RNA_protein_fa_elec_, core::scoring::methods::EnergyMethodOptions::exclude_RNA_RNA_fa_elec_, core::scoring::methods::EnergyMethodOptions::fastdens_perres_weights_, core::scoring::methods::EnergyMethodOptions::free_dof_options_, core::scoring::methods::EnergyMethodOptions::genbonded_score_full_, core::scoring::methods::EnergyMethodOptions::genbonded_score_hybrid_, core::scoring::methods::EnergyMethodOptions::geom_sol_interres_path_distance_cutoff_, core::scoring::methods::EnergyMethodOptions::geom_sol_intrares_path_distance_cutoff_, core::scoring::methods::EnergyMethodOptions::grp_cpfxn_, core::scoring::methods::EnergyMethodOptions::grpelec_context_dependent_, core::scoring::methods::EnergyMethodOptions::grpelec_fade_hbond_, core::scoring::methods::EnergyMethodOptions::grpelec_fade_param1_, core::scoring::methods::EnergyMethodOptions::grpelec_fade_param2_, core::scoring::methods::EnergyMethodOptions::grpelec_fade_type_, core::scoring::methods::EnergyMethodOptions::hbnet_bonus_ramping_function_, core::scoring::methods::EnergyMethodOptions::hbnet_max_network_size_, core::scoring::methods::EnergyMethodOptions::hbond_options_, core::scoring::methods::EnergyMethodOptions::hrf_dynamics_input_, core::scoring::methods::EnergyMethodOptions::method_weights_, core::scoring::methods::EnergyMethodOptions::mhc_epitope_setup_files_, core::scoring::methods::EnergyMethodOptions::netcharge_setup_files_, core::scoring::methods::EnergyMethodOptions::nmer_ref_seq_length_, core::scoring::methods::EnergyMethodOptions::nmer_svm_, core::scoring::methods::EnergyMethodOptions::nmer_svm_aa_matrix_, core::scoring::methods::EnergyMethodOptions::nmer_svm_aa_matrix_defined_, core::scoring::methods::EnergyMethodOptions::nmer_svm_avg_rank_as_energy_, core::scoring::methods::EnergyMethodOptions::nmer_svm_defined_, core::scoring::methods::EnergyMethodOptions::nmer_svm_list_, core::scoring::methods::EnergyMethodOptions::nmer_svm_list_defined_, core::scoring::methods::EnergyMethodOptions::nmer_svm_pssm_feat_, core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_, core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_defined_, core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_list_, core::scoring::methods::EnergyMethodOptions::nmer_svm_rank_list_defined_, core::scoring::methods::EnergyMethodOptions::nmer_svm_scorecut_, core::scoring::methods::EnergyMethodOptions::nmer_svm_scorecut_defined_, core::scoring::methods::EnergyMethodOptions::nmer_svm_term_length_, core::scoring::methods::EnergyMethodOptions::ordered_pt_wat_penalty_, core::scoring::methods::EnergyMethodOptions::ordered_wat_penalty_, core::scoring::methods::EnergyMethodOptions::pb_bound_tag_, core::scoring::methods::EnergyMethodOptions::pb_unbound_tag_, core::scoring::methods::EnergyMethodOptions::protein_dielectric_, core::scoring::methods::EnergyMethodOptions::put_intra_into_total_, core::scoring::methods::EnergyMethodOptions::rna_options_, core::scoring::methods::EnergyMethodOptions::smooth_fa_elec_, core::scoring::methods::EnergyMethodOptions::split_unfolded_label_type_, core::scoring::methods::EnergyMethodOptions::split_unfolded_value_type_, core::scoring::methods::EnergyMethodOptions::ss_weights_, core::scoring::methods::EnergyMethodOptions::target_clash_pdb_, core::scoring::methods::EnergyMethodOptions::unfolded_energies_type_, core::scoring::methods::EnergyMethodOptions::use_gen_kirkwood_, core::scoring::methods::EnergyMethodOptions::use_polarization_, core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_cone_distance_cutoff_, core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_cone_dotproduct_cutoff_, core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_containing_cones_cutoff_, core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_disabled_except_during_packing_, core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_voxel_grid_padding_, core::scoring::methods::EnergyMethodOptions::voids_penalty_energy_voxel_size_, and core::scoring::methods::EnergyMethodOptions::water_dielectric_.

bool core::scoring::methods::residues_interact ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
core::Real const  interaction_cutoff 
)
static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.OneBodyEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.TwoBodyEnergy"  )
static
static basic::Tracer core::scoring::methods::tr ( "core.scoring.methods"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.MMTorsionEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.mm.MMBondLengthEnergy"  )
static
static basic::Tracer core::scoring::methods::TR ( "core.mm.MMBondAngleEnergy"  )
static

Referenced by core::scoring::methods::MMTorsionEnergy::eval_intrares_derivatives(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::TwoBodyEnergy::eval_intrares_energy_ext(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm_list(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssms_from_options(), core::scoring::methods::NMerSVMEnergy::read_nmer_svm_list(), core::scoring::methods::NMerSVMEnergy::read_nmer_svm_rank_list(), core::scoring::methods::NMerSVMEnergy::read_nmer_svms_from_options(), core::scoring::methods::NMerRefEnergy::read_nmer_table(), core::scoring::methods::NMerRefEnergy::read_nmer_table_list(), core::scoring::methods::NMerRefEnergy::read_nmer_tables_from_options(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::TwoBodyEnergy::residue_pair_energy_ext(), core::scoring::methods::OneBodyEnergy::setup_for_derivatives_for_residue(), core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue(), core::scoring::methods::TwoBodyEnergy::setup_for_derivatives_for_residue_pair(), core::scoring::methods::TwoBodyEnergy::setup_for_scoring_for_residue(), and core::scoring::methods::TwoBodyEnergy::setup_for_scoring_for_residue_pair().