Rosetta Core  2014.35
Namespaces | Classes | Typedefs | Enumerations | Functions | Variables
core::scoring::methods Namespace Reference

Namespaces

 dfire
 

Classes

class  BBDepCartBondedParameters
 
class  BBIndepCartBondedParameters
 
class  BurialEnergy
 
class  BurialEnergyCreator
 
class  CartBondedParameters
 
class  CartesianBondedEnergy
 
class  CartesianBondedEnergyCreator
 
class  CenHBEnergy
 
class  CenHBEnergyCreator
 
class  CenPairEnergy
 
class  CenPairEnergyCreator
 
class  CenRotEnvEnergy
 
class  CenRotEnvEnergyCreator
 
class  CenRotPairEnergy
 
class  CenRotPairEnergyCreator
 
class  ChainbreakEnergy
 ChainbreakEnergy class iterates across all residues in finalize() and determines a penalty between residues i and i+1 across a cutpoint by how much their virtual atoms do not align. More...
 
class  ChainbreakEnergyCreator
 
class  ChemicalShiftAnisotropyEnergy
 
class  ChemicalShiftAnisotropyEnergyCreator
 
class  ContactOrderEnergy
 
class  ContactOrderEnergyCreator
 
class  ContextDependentLRTwoBodyEnergy
 
class  ContextDependentOneBodyEnergy
 
class  ContextDependentTwoBodyEnergy
 
class  ContextIndependentLRTwoBodyEnergy
 
class  ContextIndependentOneBodyEnergy
 
class  ContextIndependentTwoBodyEnergy
 
class  CSD_TorsionEnergy
 A knowledge-based torsional potential for small molecules derived from the Cambridge Structural Database by KWK. More...
 
class  CustomAtomPairEnergy
 
class  CustomAtomPairEnergyCreator
 
class  D2H_SA_Energy
 
class  D2H_SA_EnergyCreator
 
class  DipolarCouplingEnergy
 
class  DipolarCouplingEnergyCreator
 
class  DirectReadoutEnergy
 Implementation of Kono and Sarai's knowledge-based protein-DNA interaction energy. More...
 
class  DirectReadoutEnergyCreator
 
class  DistanceChainbreakEnergy
 DistanceChainbreakEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by how far apart their N and C atom are. More...
 
class  DistanceChainbreakEnergyCreator
 
class  DNA_BaseEnergy
 
class  DNA_BaseEnergyCreator
 
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  EnvEnergy
 
class  EnvEnergyCreator
 
class  EnvSmoothEnergy
 
class  EnvSmoothEnergyCreator
 
class  Fa_MbenvEnergy
 
class  Fa_MbenvEnergyCreator
 
class  Fa_MbsolvEnergy
 
class  Fa_MbsolvEnergyCreator
 
class  FACTSEnergy
 
class  FACTSEnergyCreator
 
class  FreeMoietyEnergy
 
class  FreeMoietyEnergyCreator
 
class  FreeResidueBonusEnergy
 
class  FreeResidueBonusEnergyCreator
 
class  GaussianOverlapEnergy
 
class  GaussianOverlapEnergyCreator
 
class  GenBornEnergy
 
class  GenBornEnergyCreator
 
class  GoapEnergy
 
class  GoapEnergyCreator
 
class  GoapRsdType
 
class  HybridVDW_Energy
 
class  HybridVDW_EnergyCreator
 
class  IdealParametersDatabase
 
class  IntermolEnergy
 
class  IntermolEnergyCreator
 
class  LinearChainbreakEnergy
 LinearChainbreakEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by how much their psueduo atoms do not align. More...
 
class  LinearChainbreakEnergyCreator
 
class  LK_BallEnergy
 
class  LK_BallEnergyCreator
 
class  LK_hack
 
class  LK_hackCreator
 
class  LK_PolarNonPolarEnergy
 
class  LK_PolarNonPolarEnergyCreator
 
class  LK_SigmoidalFunc
 
class  LKB_ResidueInfo
 
class  LKB_ResiduesInfo
 
class  LKB_ResPairMinData
 
class  LongRangeTwoBodyEnergy
 
class  MembraneCbetaEnergy
 
class  MembraneCbetaEnergyCreator
 
class  MembraneCenPairEnergy
 
class  MembraneCenPairEnergyCreator
 
class  MembraneEnvEnergy
 
class  MembraneEnvEnergyCreator
 
class  MembraneEnvPenalties
 
class  MembraneEnvPenaltiesCreator
 
class  MembraneEnvSmoothEnergy
 
class  MembraneEnvSmoothEnergyCreator
 
class  MembraneLipo
 
class  MembraneLipoCreator
 
class  MetalloPlacementEnergy
 
class  MissingEnergy
 
class  MissingEnergyCreator
 
class  MMBondAngleEnergy
 
class  MMBondAngleEnergyCreator
 
class  MMBondLengthEnergy
 
class  MMBondLengthEnergyCreator
 
class  MMLJEnergyInter
 
class  MMLJEnergyInterCreator
 
class  MMLJEnergyIntra
 
class  MMLJEnergyIntraCreator
 
class  MMTorsionEnergy
 
class  MMTorsionEnergyCreator
 
class  NMerPSSMEnergy
 
class  NMerPSSMEnergyCreator
 
class  NMerRefEnergy
 
class  NMerRefEnergyCreator
 
class  NMerSVMEnergy
 
class  NMerSVMEnergyCreator
 
class  OmegaTetherEnergy
 
class  OmegaTetherEnergyCreator
 
class  OneBodyEnergy
 
class  OtherPoseEnergy
 
class  OtherPoseEnergyCreator
 
class  P_AA_Energy
 
class  P_AA_EnergyCreator
 
class  P_AA_pp_Energy
 
class  P_AA_pp_EnergyCreator
 
class  PackStatEnergy
 
class  PackStatEnergyCreator
 
class  PairEnergy
 
class  PairEnergyCreator
 
class  PBLifetimeCache
 
class  PeptideBondEnergy
 PeptideBondEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by the distance the C-N bond. Evantually I'd also like to add bond angle constraints as well, but that's handled by OmegaTether at the moment. More...
 
class  PeptideBondEnergyCreator
 
class  pHEnergy
 
class  pHEnergyCreator
 
class  PoissonBoltzmannEnergy
 
class  PoissonBoltzmannEnergyCreator
 
class  ProClosureEnergy
 
class  ProClosureEnergyCreator
 
class  ProQ_Energy
 
class  ProQ_EnergyCreator
 
class  PyContextIndependentOneBodyEnergy
 
class  PyContextIndependentTwoBodyEnergy
 
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...
 
class  Rama2BOffsetEnergy
 
class  Rama2BOffsetEnergyCreator
 
class  RamachandranEnergy
 
class  RamachandranEnergy2B
 
class  RamachandranEnergy2BCreator
 
class  RamachandranEnergyCreator
 
class  ReferenceEnergy
 
class  ReferenceEnergyCreator
 
class  ReferenceEnergyNoncanonical
 
class  ReferenceEnergyNoncanonicalCreator
 
class  ResidualDipolarCouplingEnergy
 
class  ResidualDipolarCouplingEnergy_Rohl
 
class  ResidualDipolarCouplingEnergy_RohlCreator
 
class  ResidualDipolarCouplingEnergyCreator
 
class  ResidualDipolarCouplingEnergyRigidSegments
 
class  ResidueCartBondedParameters
 
class  RG_Energy
 
class  RG_Energy_Fast
 
class  RG_Energy_FastCreator
 
class  RG_Local_MinData
 
class  RG_LocalEnergy
 
class  RG_LocalEnergyCreator
 
class  RG_MinData
 
class  RMS_Energy
 
class  RMS_EnergyCreator
 
class  SA_Energy
 
class  SA_EnergyCreator
 
class  SecondaryStructureEnergy
 
class  SecondaryStructureEnergyCreator
 
class  SequenceDependentRefEnergy
 
class  SequenceDependentRefEnergyCreator
 
class  ShortRangeTwoBodyEnergy
 
class  SmoothCenPairEnergy
 
class  SmoothCenPairEnergyCreator
 
class  SmoothEnvEnergy
 
class  SmoothEnvEnergyCreator
 
class  SuckerEnergy
 
class  SuckerEnergyCreator
 
class  SymmetricLigandEnergy
 
class  SymmetricLigandEnergyCreator
 
class  TwoBodyEnergy
 
class  UnfoldedStateEnergy
 
class  UnfoldedStateEnergyCreator
 
class  WaterAdductHBondEnergy
 
class  WaterAdductHBondEnergyCreator
 
class  WaterAdductIntraEnergy
 
class  WaterAdductIntraEnergyCreator
 
class  WaterBuilder
 
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...
 
class  YHHPlanarityEnergy
 
class  YHHPlanarityEnergyCreator
 

Typedefs

typedef
utility::pointer::access_ptr
< CartBondedParameters
CartBondedParametersAP
 
typedef
utility::pointer::access_ptr
< CartBondedParameters const > 
CartBondedParametersCAP
 
typedef
utility::pointer::owning_ptr
< CartBondedParameters
CartBondedParametersOP
 
typedef
utility::pointer::owning_ptr
< CartBondedParameters const > 
CartBondedParametersCOP
 
typedef
utility::pointer::access_ptr
< ResidueCartBondedParameters
ResidueCartBondedParametersAP
 
typedef
utility::pointer::access_ptr
< ResidueCartBondedParameters
const > 
ResidueCartBondedParametersCAP
 
typedef
utility::pointer::owning_ptr
< ResidueCartBondedParameters
ResidueCartBondedParametersOP
 
typedef
utility::pointer::owning_ptr
< ResidueCartBondedParameters
const > 
ResidueCartBondedParametersCOP
 
typedef
utility::pointer::access_ptr
< IdealParametersDatabase
IdealParametersDatabaseAP
 
typedef
utility::pointer::access_ptr
< IdealParametersDatabase
const > 
IdealParametersDatabaseCAP
 
typedef
utility::pointer::owning_ptr
< IdealParametersDatabase
IdealParametersDatabaseOP
 
typedef
utility::pointer::owning_ptr
< IdealParametersDatabase
const > 
IdealParametersDatabaseCOP
 
typedef
utility::pointer::access_ptr
< CartesianBondedEnergy
CartesianBondedEnergyAP
 
typedef
utility::pointer::access_ptr
< CartesianBondedEnergy const > 
CartesianBondedEnergyCAP
 
typedef
utility::pointer::owning_ptr
< CartesianBondedEnergy
CartesianBondedEnergyOP
 
typedef
utility::pointer::owning_ptr
< CartesianBondedEnergy const > 
CartesianBondedEnergyCOP
 
typedef
utility::pointer::owning_ptr
< ChemicalShiftAnisotropyEnergy
ChemicalShiftAnisotropyEnergyOP
 
typedef
utility::pointer::owning_ptr
< ContextDependentLRTwoBodyEnergy
ContextDependentLRTwoBodyEnergyOP
 
typedef
utility::pointer::owning_ptr
< ContextDependentLRTwoBodyEnergy
const > 
ContextDependentLRTwoBodyEnergyCOP
 
typedef
utility::pointer::owning_ptr
< ContextDependentOneBodyEnergy
ContextDependentOneBodyEnergyOP
 
typedef
utility::pointer::owning_ptr
< ContextDependentTwoBodyEnergy
ContextDependentTwoBodyEnergyOP
 
typedef
utility::pointer::owning_ptr
< ContextDependentTwoBodyEnergy
const > 
ContextDependentTwoBodyEnergyCOP
 
typedef
utility::pointer::owning_ptr
< ContextIndependentLRTwoBodyEnergy
ContextIndependentLRTwoBodyEnergyOP
 
typedef
utility::pointer::owning_ptr
< ContextIndependentLRTwoBodyEnergy
const > 
ContextIndependentLRTwoBodyEnergyCOP
 
typedef
utility::pointer::owning_ptr
< ContextIndependentOneBodyEnergy
ContextIndependentOneBodyEnergyOP
 
typedef
utility::pointer::owning_ptr
< ContextIndependentOneBodyEnergy
const > 
ContextIndependentOneBodyEnergyCOP
 
typedef
utility::pointer::owning_ptr
< ContextIndependentTwoBodyEnergy
ContextIndependentTwoBodyEnergyOP
 
typedef
utility::pointer::owning_ptr
< ContextIndependentTwoBodyEnergy
const > 
ContextIndependentTwoBodyEnergyCOP
 
typedef
utility::pointer::owning_ptr
< CSD_TorsionEnergy
CSD_TorsionEnergyOP
 
typedef
utility::pointer::owning_ptr
< CSD_TorsionEnergy const > 
CSD_TorsionEnergyCOP
 
typedef
utility::pointer::owning_ptr
< PoissonBoltzmannEnergy
PoissonBoltzmannEnergyOP
 
typedef
utility::pointer::owning_ptr
< PoissonBoltzmannEnergy const > 
PoissonBoltzmannEnergyCOP
 
typedef
utility::pointer::owning_ptr
< DipolarCouplingEnergy
DipolarCouplingEnergyOP
 
typedef
utility::pointer::owning_ptr
< EnergyMethod
EnergyMethodOP
 
typedef
utility::pointer::owning_ptr
< EnergyMethod const > 
EnergyMethodCOP
 
typedef
utility::pointer::owning_ptr
< EnergyMethodCreator
EnergyMethodCreatorOP
 
typedef
utility::pointer::owning_ptr
< EnergyMethodCreator const > 
EnergyMethodCreatorCOP
 
typedef
utility::pointer::owning_ptr
< EnergyMethodOptions
EnergyMethodOptionsOP
 
typedef
utility::pointer::owning_ptr
< EnergyMethodOptions const > 
EnergyMethodOptionsCOP
 
typedef
utility::pointer::owning_ptr
< Fa_MbenvEnergy
Fa_MbenvEnergyOP
 
typedef
utility::pointer::owning_ptr
< GoapRsdType
GoapRsdTypeOP
 
typedef
utility::pointer::owning_ptr
< GoapRsdType const > 
GoapRsdTypeCOP
 
typedef
utility::pointer::owning_ptr
< GoapEnergy
GoapEnergyOP
 
typedef std::map< std::string,
GoapRsdTypeOP
GoapRsdTypeMap
 
typedef
utility::pointer::owning_ptr
< LKB_ResPairMinData
LKB_ResPairMinDataOP
 
typedef
utility::pointer::owning_ptr
< LKB_ResPairMinData const > 
LKB_ResPairMinDataCOP
 
typedef utility::vector1
< WaterBuilder
WaterBuilders
 
typedef
utility::pointer::owning_ptr
< LKB_ResidueInfo
LKB_ResidueInfoOP
 
typedef
utility::pointer::owning_ptr
< const LKB_ResidueInfo
LKB_ResidueInfoCOP
 
typedef LKB_ResiduesInfo LKB_PoseInfo
 
typedef LKB_ResiduesInfo LKB_RotamerSetInfo
 
typedef
utility::pointer::owning_ptr
< LKB_PoseInfo
LKB_PoseInfoOP
 
typedef
utility::pointer::owning_ptr
< LKB_RotamerSetInfo
LKB_RotamerSetInfoOP
 
typedef
utility::pointer::owning_ptr
< LongRangeTwoBodyEnergy
LongRangeTwoBodyEnergyOP
 
typedef
utility::pointer::owning_ptr
< LongRangeTwoBodyEnergy const > 
LongRangeTwoBodyEnergyCOP
 
typedef
utility::pointer::access_ptr
< MMBondAngleEnergy
MMBondAngleEnergyAP
 
typedef
utility::pointer::access_ptr
< MMBondAngleEnergy const > 
MMBondAngleEnergyCAP
 
typedef
utility::pointer::owning_ptr
< MMBondAngleEnergy
MMBondAngleEnergyOP
 
typedef
utility::pointer::owning_ptr
< MMBondAngleEnergy const > 
MMBondAngleEnergyCOP
 
typedef
utility::pointer::access_ptr
< MMBondLengthEnergy
MMBondLengthEnergyAP
 
typedef
utility::pointer::access_ptr
< MMBondLengthEnergy const > 
MMBondLengthEnergyCAP
 
typedef
utility::pointer::owning_ptr
< MMBondLengthEnergy
MMBondLengthEnergyOP
 
typedef
utility::pointer::owning_ptr
< MMBondLengthEnergy const > 
MMBondLengthEnergyCOP
 
typedef
utility::pointer::access_ptr
< MMLJEnergyInter
MMLJEnergyInterAP
 
typedef
utility::pointer::access_ptr
< MMLJEnergyInter const > 
MMLJEnergyInterCAP
 
typedef
utility::pointer::owning_ptr
< MMLJEnergyInter
MMLJEnergyInterOP
 
typedef
utility::pointer::owning_ptr
< MMLJEnergyInter const > 
MMLJEnergyInterCOP
 
typedef
utility::pointer::access_ptr
< MMLJEnergyIntra
MMLJEnergyIntraAP
 
typedef
utility::pointer::access_ptr
< MMLJEnergyIntra const > 
MMLJEnergyIntraCAP
 
typedef
utility::pointer::owning_ptr
< MMLJEnergyIntra
MMLJEnergyIntraOP
 
typedef
utility::pointer::owning_ptr
< MMLJEnergyIntra const > 
MMLJEnergyIntraCOP
 
typedef std::pair
< mm::mm_torsion_atom_quad,
core::Real
mm_torsion_atom_quad_angle_pair
 
typedef utility::vector1
< mm_torsion_atom_quad_angle_pair >
::const_iterator 
mmtaqap_iter
 
typedef
utility::pointer::access_ptr
< MMTorsionEnergy
MMTorsionEnergyAP
 
typedef
utility::pointer::access_ptr
< MMTorsionEnergy const > 
MMTorsionEnergyCAP
 
typedef
utility::pointer::owning_ptr
< MMTorsionEnergy
MMTorsionEnergyOP
 
typedef
utility::pointer::owning_ptr
< MMTorsionEnergy const > 
MMTorsionEnergyCOP
 
typedef
utility::pointer::owning_ptr
< NMerPSSMEnergy
NMerPSSMEnergyOP
 
typedef
utility::pointer::owning_ptr
< NMerPSSMEnergy const > 
NMerPSSMEnergyCOP
 
typedef
utility::pointer::owning_ptr
< NMerRefEnergy
NMerRefEnergyOP
 
typedef
utility::pointer::owning_ptr
< NMerRefEnergy const > 
NMerRefEnergyCOP
 
typedef
utility::pointer::owning_ptr
< NMerSVMEnergy
NMerSVMEnergyOP
 
typedef
utility::pointer::owning_ptr
< NMerSVMEnergy const > 
NMerSVMEnergyCOP
 
typedef
utility::pointer::owning_ptr
< OmegaTetherEnergy
OmegaTetherEnergyOP
 
typedef
utility::pointer::owning_ptr
< OmegaTetherEnergy const > 
OmegaTetherEnergyCOP
 
typedef
utility::pointer::owning_ptr
< OneBodyEnergy
OneBodyEnergyOP
 
typedef
utility::pointer::owning_ptr
< OneBodyEnergy const > 
OneBodyEnergyCOP
 
typedef
utility::pointer::owning_ptr
< OtherPoseEnergy
OtherPoseEnergyOP
 
typedef
utility::pointer::owning_ptr
< OtherPoseEnergy const > 
OtherPoseEnergyCOP
 
typedef
utility::pointer::owning_ptr
< P_AA_Energy
P_AA_EnergyOP
 
typedef
utility::pointer::owning_ptr
< P_AA_pp_Energy
P_AA_pp_EnergyOP
 
typedef
utility::pointer::owning_ptr
< pHEnergy
pHEnergyOP
 
typedef
utility::pointer::access_ptr
< PoissonBoltzmannEnergy
PoissonBoltzmannEnergyAP
 
typedef
utility::pointer::access_ptr
< PoissonBoltzmannEnergy const > 
PoissonBoltzmannEnergyCAP
 
typedef
utility::pointer::owning_ptr
< PBLifetimeCache
PBLifetimeCacheOP
 
typedef
utility::pointer::owning_ptr
< PBLifetimeCache const > 
PBLifetimeCacheCOP
 
typedef
utility::pointer::access_ptr
< PBLifetimeCache
PBLifetimeCacheAP
 
typedef
utility::pointer::access_ptr
< PBLifetimeCache const > 
PBLifetimeCacheCAP
 
typedef
utility::pointer::owning_ptr
< ProClosureEnergy
ProClosureEnergyOP
 
typedef
utility::pointer::owning_ptr
< ProClosureEnergy const > 
ProClosureEnergyCOP
 
typedef
utility::pointer::access_ptr
< Rama2BOffsetEnergy
Rama2BOffsetEnergyAP
 
typedef
utility::pointer::access_ptr
< Rama2BOffsetEnergy const > 
Rama2BOffsetEnergyCAP
 
typedef
utility::pointer::owning_ptr
< Rama2BOffsetEnergy
Rama2BOffsetEnergyOP
 
typedef
utility::pointer::owning_ptr
< Rama2BOffsetEnergy const > 
Rama2BOffsetEnergyCOP
 
typedef
utility::pointer::owning_ptr
< RamachandranEnergy
RamachandranEnergyOP
 
typedef
utility::pointer::owning_ptr
< RamachandranEnergy const > 
RamachandranEnergyCOP
 
typedef
utility::pointer::owning_ptr
< RamachandranEnergy2B
RamachandranEnergy2BOP
 
typedef
utility::pointer::owning_ptr
< RamachandranEnergy2B const > 
RamachandranEnergy2BCOP
 
typedef
utility::pointer::owning_ptr
< ReferenceEnergy
ReferenceEnergyOP
 
typedef
utility::pointer::owning_ptr
< ReferenceEnergy const > 
ReferenceEnergyCOP
 
typedef
utility::pointer::owning_ptr
< ReferenceEnergyNoncanonical
ReferenceEnergyNoncanonicalOP
 
typedef
utility::pointer::owning_ptr
< ReferenceEnergyNoncanonical
const > 
ReferenceEnergyNoncanonicalCOP
 
typedef
utility::pointer::owning_ptr
< ResidualDipolarCouplingEnergy
ResidualDipolarCouplingEnergyOP
 
typedef
utility::pointer::owning_ptr
< ResidualDipolarCouplingEnergyRigidSegments
ResidualDipolarCouplingEnergyRigidSegmentsOP
 
typedef
utility::pointer::owning_ptr
< RG_MinData
RG_MinDataOP
 
typedef
utility::pointer::owning_ptr
< RG_Local_MinData
RG_Local_MinDataOP
 
typedef
utility::pointer::owning_ptr
< SequenceDependentRefEnergy
SequenceDependentRefEnergyOP
 
typedef
utility::pointer::owning_ptr
< SequenceDependentRefEnergy
const > 
SequenceDependentRefEnergyCOP
 
typedef
utility::pointer::owning_ptr
< ShortRangeTwoBodyEnergy
ShortRangeTwoBodyEnergyOP
 
typedef
utility::pointer::owning_ptr
< ShortRangeTwoBodyEnergy
const > 
ShortRangeTwoBodyEnergyCOP
 
typedef
utility::pointer::owning_ptr
< TwoBodyEnergy
TwoBodyEnergyOP
 
typedef
utility::pointer::owning_ptr
< TwoBodyEnergy const > 
TwoBodyEnergyCOP
 
typedef
utility::pointer::owning_ptr
< UnfoldedStateEnergy
UnfoldedStateEnergyOP
 
typedef
utility::pointer::owning_ptr
< WaterAdductIntraEnergy
WaterAdductIntraEnergyOP
 
typedef
utility::pointer::owning_ptr
< WholeStructureEnergy
WholeStructureEnergyOP
 
typedef
utility::pointer::owning_ptr
< YHHPlanarityEnergy
YHHPlanarityEnergyOP
 

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,
  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, PB_elec_lr, cart_bonded_lr,
  rama2b_lr, rna_suite_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

std::string get_restag (core::chemical::ResidueType const &restype)
 helper function More...
 
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 (const core::pose::Pose &pose, const core::kinematics::FoldTree &, utility::vector1< int > *cutpoints)
 
void swap_seqpos (core::Size &seqpos1, core::Size &seqpos2)
 
std::string const dna_deriv_atom (" C5 ")
 the atom through which the knowledge based potential applies a force More...
 
bool count_pair_bs (Size const pos1, Size const pos2, BasePartner const &partner)
 ordered!!!! requires pos1<pos2 More...
 
BasePartner const & retrieve_base_partner_from_pose_inline (pose::Pose const &pose)
 same as dna::retrieve_base_partner_from_pose 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)
 
Real sqr (Real x)
 
bool count_atom (int const &atype)
 
LKB_RotamerSetInfo const & retrieve_lkb_rotamer_set_info (conformation::RotamerSetBase const &set)
 inline retrieval functions here: More...
 
LKB_ResidueInfo const & retrieve_lkb_residue_info (pose::Pose const &pose, Size const seqpos)
 
LKB_ResidueInforetrieve_nonconst_lkb_residue_info (pose::Pose &pose, Size const seqpos)
 
LKB_ResPairMinDataretrieve_nonconst_lkb_pairdata (ResPairMinimizationData &pairdata)
 
LKB_ResPairMinData const & retrieve_lkb_pairdata (ResPairMinimizationData const &pairdata)
 
LKB_ResidueInforetrieve_nonconst_lkb_resdata (ResSingleMinimizationData &resdata)
 
LKB_ResidueInfo const & retrieve_lkb_resdata (ResSingleMinimizationData const &resdata)
 
LKB_ResidueInfoCOP retrieve_lkb_resdata_ptr (ResSingleMinimizationData const &resdata)
 
void compute_and_store_pose_waters (pose::Pose &pose)
 
scoring::etable::count_pair::CPCrossoverBehavior determine_crossover_behavior (conformation::Residue const &res1, conformation::Residue const &res2, bool const use_intra_dna_cp_crossover_4)
 
Size get_parallel_h_for_arg (chemical::ResidueType const &rsd_type, Size const hatm)
 
void apply_lk_ball_fraction_weight_for_hbonds (Size const hatm, conformation::Residue const &don_rsd, Size const aatm, conformation::Residue const &acc_rsd, Vector const &hatm_xyz, Vector const &datm_xyz, Real &unweighted_energy, bool const evaluate_derivative, hbonds::HBondDerivs &hbderivs, Real &don_lk_fraction, Real &acc_lk_fraction)
 this is a helper function for hbonds More...
 
Vector build_optimal_water_O_on_donor (Vector const &hxyz, Vector const &dxyz)
 
utility::vector1< Vectorbuild_optimal_water_Os_on_acceptor (Size const acc_atm, conformation::Residue const &acc_rsd, Vector const &a_xyz, Vector b1_xyz, Vector b2_xyz, chemical::Hybridization const &hybrid)
 
void setup_water_builders_for_residue_type (ResidueType const &rsd_type, bool const sidechain_only, utility::vector1< WaterBuilders > &rsd_water_builders)
 
template<class T >
utility::pointer::access_ptr< T_AP (T &o)
 
template<class T >
utility::pointer::access_ptr
< T const > 
_CAP (T const &o)
 
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)
 

Variables

static basic::Tracer TR ("core.scoring.CartesianBondedEnergy")
 
static basic::Tracer GEOMETRIES ("core.scoring.CartesianBondedEnergy.GEOMETRIES")
 
static const Real K_LENGTH =300.0
 
static const Real K_ANGLE =80.0
 
static const Real K_TORSION =20.0
 
static const Real K_TORSION_PROTON =10.0
 
static const Real K_TORSION_IMPROPER =40.0
 
static basic::Tracer tr ("core.scoring.methods.CustomAtomPairEnergy")
 
static basic::Tracer TR ("core.scoring.methods.D2H_SA_Energy.cc")
 
Distance const start_sig = 9.8
 
Distance const end_sig = 10.2
 
DistanceSquared const start_sig2 = start_sig*start_sig
 
DistanceSquared const end_sig2 = end_sig*end_sig
 
core::Real const envdata [20][40]
 
static basic::Tracer TR ("core.scoring.GoapEnergy")
 
Real const vdw_scale_factor (0.8)
 
static basic::Tracer tr ("core.scoring.LinearChainbreak", basic::t_info)
 
static basic::Tracer TR ("core.scoring.methods.LK_BallEnergy")
 
static basic::Tracer TR ("core.scoring.methods.LK_BallInfo")
 
static Real const optimal_water_distance (2.65)
 
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.ProQ_Energy.cc")
 
static basic::Tracer TR ("core.scoring.Rama2BOffsetEnergy")
 
static basic::Tracer tr ("core.scoring.methods")
 

Typedef Documentation

Enumeration Type Documentation

Enumerator
etable_method 
dunbrack_method 
hbond_method 
elec_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 
PB_elec_lr 
cart_bonded_lr 
rama2b_lr 
rna_suite_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

template<class T >
utility::pointer::access_ptr<T> core::scoring::methods::_AP ( T o)
template<class T >
utility::pointer::access_ptr<T const > core::scoring::methods::_CAP ( T const &  o)
void core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds ( Size const  hatm,
conformation::Residue const &  don_rsd,
Size const  aatm,
conformation::Residue const &  acc_rsd,
Vector const &  hatm_xyz,
Vector const &  datm_xyz,
Real unweighted_energy,
bool const  evaluate_derivative,
hbonds::HBondDerivs &  hbderivs,
Real don_fraction,
Real acc_fraction 
)

this is a helper function for hbonds

hack to improve geometries of hbonds: apply an additional weighting factor which is used in LK_BallEnergy Do this for sidechain SP2 or Ring acceptors Do this for all sidechain donors

NOTE: also excluding multiple parallel Arg hbonds

Note
For the deriv calculation, we assume that the deriv passed in has already been evaluated by hb_energy_deriv and thus represents the deriv of the unweighted energy considering the donor as the moving atom.

References core::conformation::Residue::aa(), core::chemical::aa_arg, core::conformation::Residue::abase2(), core::scoring::hbonds::HBondDerivs::abase2_deriv, core::scoring::hbonds::HBondDerivs::abase_deriv, core::scoring::hbonds::HBondDerivs::acc_deriv, core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_type(), chemical, core::scoring::hbonds::HBondDerivs::don_deriv, numeric::xyzVector< class >::dot(), core::scoring::methods::LK_BallEnergy::eval_lk_ball_fraction_deriv(), core::scoring::DerivVectorPair::f1(), core::scoring::DerivVectorPair::f2(), get_parallel_h_for_arg(), core::scoring::hbonds::HBondDerivs::h_deriv, core::chemical::AtomType::hybridization(), core::conformation::Residue::is_protein(), numeric::conversions::radians(), core::chemical::RING_HYBRID, core::chemical::SP2_HYBRID, core::conformation::Atom::type(), core::conformation::Residue::type(), utility_exit_with_message, and core::conformation::Residue::xyz().

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 
)
Vector core::scoring::methods::build_optimal_water_O_on_donor ( Vector const &  hxyz,
Vector const &  dxyz 
)

The next two functions were taken from protocols/water/rotamer_building_functions.cc with slight modifications

References optimal_water_distance.

Referenced by setup_water_builders_for_residue_type().

utility::vector1< Vector > core::scoring::methods::build_optimal_water_Os_on_acceptor ( Size const  acc_atm,
conformation::Residue const &  acc_rsd,
Vector const &  a_xyz,
Vector  b1_xyz,
Vector  b2_xyz,
chemical::Hybridization const &  hybrid 
)
void core::scoring::methods::compute_and_store_pose_waters ( pose::Pose &  pose)
bool core::scoring::methods::count_atom ( int const &  atype)
inline
bool core::scoring::methods::count_pair_bs ( Size const  pos1,
Size const  pos2,
BasePartner const &  partner 
)
inline
scoring::etable::count_pair::CPCrossoverBehavior core::scoring::methods::determine_crossover_behavior ( conformation::Residue const &  res1,
conformation::Residue const &  res2,
bool const  use_intra_dna_cp_crossover_4 
)
std::string const core::scoring::methods::dna_deriv_atom ( " C5 "  )

the atom through which the knowledge based potential applies a force

Referenced by core::scoring::methods::DNA_BaseEnergy::eval_atom_derivative().

void core::scoring::methods::find_cutpoint_variants ( const core::pose::Pose pose,
const core::kinematics::FoldTree ,
utility::vector1< int > *  cutpoints 
)
Size core::scoring::methods::get_parallel_h_for_arg ( chemical::ResidueType const &  rsd_type,
Size const  hatm 
)
core::Real core::scoring::methods::get_residue_weight_by_ss ( const char  ss)
std::string core::scoring::methods::get_restag ( core::chemical::ResidueType const &  restype)
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::operator!= ( EnergyMethodOptions const &  a,
EnergyMethodOptions const &  b 
)
std::ostream & core::scoring::methods::operator<< ( std::ostream &  out,
EnergyMethodOptions const &  options 
)
bool core::scoring::methods::operator== ( EnergyMethodOptions const &  a,
EnergyMethodOptions const &  b 
)

used inside ScoreFunctionInfo::operator==

References core::scoring::methods::EnergyMethodOptions::analytic_etable_evaluation_, 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_len_, core::scoring::methods::EnergyMethodOptions::cartbonded_linear_, core::scoring::methods::EnergyMethodOptions::cartbonded_proton_, core::scoring::methods::EnergyMethodOptions::cartbonded_tors_, core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep_, core::scoring::methods::EnergyMethodOptions::elec_die_, 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::etable_options_, core::scoring::methods::EnergyMethodOptions::etable_type_, core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA_, core::scoring::methods::EnergyMethodOptions::exclude_monomer_fa_elec_, core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_elec_, core::scoring::methods::EnergyMethodOptions::hbond_options_, core::scoring::methods::EnergyMethodOptions::intrares_elec_correction_scale_, core::scoring::methods::EnergyMethodOptions::method_weights_, core::scoring::methods::EnergyMethodOptions::pb_bound_tag_, core::scoring::methods::EnergyMethodOptions::pb_unbound_tag_, core::scoring::methods::EnergyMethodOptions::smooth_fa_elec_, core::scoring::methods::EnergyMethodOptions::ss_weights_, and core::scoring::methods::EnergyMethodOptions::unfolded_energies_type_.

bool core::scoring::methods::residues_interact ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
core::Real const  interaction_cutoff 
)
BasePartner const& core::scoring::methods::retrieve_base_partner_from_pose_inline ( pose::Pose const &  pose)
inline
LKB_ResPairMinData const& core::scoring::methods::retrieve_lkb_pairdata ( ResPairMinimizationData const &  pairdata)
inline
LKB_ResidueInfo const& core::scoring::methods::retrieve_lkb_resdata ( ResSingleMinimizationData const &  resdata)
inline
LKB_ResidueInfoCOP core::scoring::methods::retrieve_lkb_resdata_ptr ( ResSingleMinimizationData const &  resdata)
inline
LKB_ResidueInfo const& core::scoring::methods::retrieve_lkb_residue_info ( pose::Pose const &  pose,
Size const  seqpos 
)
inline
LKB_RotamerSetInfo const& core::scoring::methods::retrieve_lkb_rotamer_set_info ( conformation::RotamerSetBase const &  set)
inline
LKB_ResPairMinData& core::scoring::methods::retrieve_nonconst_lkb_pairdata ( ResPairMinimizationData &  pairdata)
inline
LKB_ResidueInfo& core::scoring::methods::retrieve_nonconst_lkb_resdata ( ResSingleMinimizationData &  resdata)
inline
LKB_ResidueInfo& core::scoring::methods::retrieve_nonconst_lkb_residue_info ( pose::Pose &  pose,
Size const  seqpos 
)
inline
void core::scoring::methods::setup_water_builders_for_residue_type ( ResidueType const &  rsd_type,
bool const  sidechain_only,
utility::vector1< WaterBuilders > &  rsd_water_builders 
)
Real core::scoring::methods::sqr ( Real  x)
inline
void core::scoring::methods::swap_seqpos ( core::Size seqpos1,
core::Size seqpos2 
)

Variable Documentation

Distance const core::scoring::methods::end_sig = 10.2
DistanceSquared const core::scoring::methods::end_sig2 = end_sig*end_sig
core::Real const core::scoring::methods::envdata[20][40]
Initial value:
= {
{ 3.46, 3.33, 3.05, 2.54, 1.89, 1.30, 0.90, 0.65, 0.48, 0.35, 0.27, 0.23, 0.21, 0.21, 0.18, 0.16, 0.11, 0.06,-0.01,-0.09,-0.16,-0.21,-0.25,-0.26,-0.28,-0.28,-0.28,-0.29,-0.30,-0.33,-0.39,-0.46,-0.55,-0.63,-0.70,-0.74,-0.76,-0.81,-0.89,-1.00 },
{ 2.60, 2.54, 2.47, 2.39, 2.29, 2.22, 2.18, 2.11, 1.97, 1.76, 1.55, 1.37, 1.20, 1.01, 0.81, 0.60, 0.40, 0.19,-0.01,-0.19,-0.33,-0.44,-0.51,-0.57,-0.62,-0.66,-0.69,-0.73,-0.74,-0.75,-0.73,-0.74,-0.76,-0.84,-0.93,-1.04,-1.14,-1.22,-1.27,-1.28 },
{-0.50,-0.47,-0.45,-0.43,-0.43,-0.43,-0.45,-0.48,-0.50,-0.52,-0.51,-0.48,-0.44,-0.38,-0.30,-0.22,-0.11, 0.00, 0.13, 0.27, 0.41, 0.54, 0.66, 0.79, 0.91, 1.02, 1.09, 1.13, 1.16, 1.18, 1.20, 1.24, 1.29, 1.35, 1.41, 1.46, 1.49, 1.50, 1.47, 1.43 },
{-0.81,-0.82,-0.82,-0.80,-0.80,-0.80,-0.81,-0.80,-0.77,-0.71,-0.63,-0.54,-0.45,-0.35,-0.23,-0.09, 0.07, 0.23, 0.40, 0.57, 0.74, 0.91, 1.06, 1.19, 1.32, 1.42, 1.53, 1.62, 1.68, 1.71, 1.74, 1.78, 1.82, 1.85, 1.88, 1.89, 1.88, 1.87, 1.86, 1.88 },
{ 0.37, 0.36, 0.36, 0.38, 0.45, 0.56, 0.72, 0.88, 1.00, 1.05, 1.04, 0.97, 0.87, 0.74, 0.59, 0.45, 0.31, 0.19, 0.08,-0.03,-0.14,-0.25,-0.34,-0.43,-0.51,-0.59,-0.66,-0.72,-0.76,-0.76,-0.72,-0.64,-0.54,-0.43,-0.37,-0.32,-0.30,-0.26,-0.25,-0.24 },
{ 2.37, 2.32, 2.26, 2.10, 1.78, 1.32, 0.86, 0.49, 0.26, 0.11, 0.00,-0.07,-0.11,-0.14,-0.14,-0.13,-0.12,-0.11,-0.10,-0.07,-0.05,-0.02, 0.02, 0.06, 0.09, 0.09, 0.08, 0.05, 0.00,-0.08,-0.15,-0.26,-0.37,-0.51,-0.64,-0.76,-0.84,-0.92,-0.99,-1.06 },
{-0.42,-0.35,-0.32,-0.32,-0.31,-0.28,-0.21,-0.15,-0.09,-0.06,-0.06,-0.08,-0.11,-0.13,-0.15,-0.17,-0.16,-0.14,-0.10,-0.05, 0.01, 0.09, 0.18, 0.25, 0.31, 0.34, 0.35, 0.35, 0.34, 0.34, 0.35, 0.36, 0.37, 0.36, 0.34, 0.33, 0.30, 0.26, 0.22, 0.18 },
{ 1.39, 1.37, 1.35, 1.33, 1.32, 1.32, 1.32, 1.31, 1.28, 1.23, 1.15, 1.07, 0.97, 0.86, 0.74, 0.61, 0.48, 0.35, 0.21, 0.07,-0.06,-0.18,-0.30,-0.42,-0.54,-0.65,-0.76,-0.86,-0.94,-1.00,-1.04,-1.04,-1.03,-1.00,-0.95,-0.90,-0.85,-0.79,-0.73,-0.64 },
{-1.55,-1.60,-1.61,-1.57,-1.49,-1.36,-1.22,-1.05,-0.89,-0.73,-0.61,-0.50,-0.40,-0.28,-0.14, 0.03, 0.22, 0.43, 0.66, 0.89, 1.12, 1.33, 1.52, 1.71, 1.87, 2.00, 2.08, 2.14, 2.18, 2.21, 2.22, 2.23, 2.27, 2.32, 2.41, 2.49, 2.56, 2.60, 2.61, 2.61 },
{ 2.77, 2.62, 2.40, 2.11, 1.83, 1.62, 1.48, 1.38, 1.29, 1.19, 1.10, 0.99, 0.85, 0.68, 0.50, 0.32, 0.15, 0.00,-0.12,-0.23,-0.32,-0.41,-0.49,-0.55,-0.59,-0.60,-0.57,-0.52,-0.44,-0.36,-0.27,-0.17,-0.05, 0.08, 0.23, 0.36, 0.47, 0.55, 0.60, 0.62 },
{ 0.99, 0.98, 0.96, 0.95, 0.94, 0.92, 0.91, 0.89, 0.87, 0.85, 0.82, 0.77, 0.70, 0.61, 0.51, 0.40, 0.30, 0.20, 0.11, 0.02,-0.07,-0.15,-0.24,-0.33,-0.42,-0.52,-0.61,-0.69,-0.78,-0.85,-0.90,-0.91,-0.90,-0.87,-0.81,-0.72,-0.60,-0.49,-0.40,-0.33 },
{-0.17,-0.21,-0.22,-0.24,-0.26,-0.30,-0.33,-0.34,-0.35,-0.35,-0.34,-0.32,-0.29,-0.26,-0.22,-0.18,-0.13,-0.08,-0.01, 0.08, 0.17, 0.27, 0.38, 0.49, 0.58, 0.65, 0.71, 0.75, 0.76, 0.74, 0.74, 0.75, 0.79, 0.81, 0.84, 0.86, 0.89, 0.89, 0.86, 0.83 },
{ 0.06, 0.04, 0.02,-0.02,-0.09,-0.20,-0.31,-0.37,-0.37,-0.32,-0.26,-0.22,-0.17,-0.14,-0.11,-0.09,-0.07,-0.04,-0.01, 0.03, 0.08, 0.15, 0.22, 0.30, 0.37, 0.42, 0.46, 0.50, 0.55, 0.59, 0.61, 0.61, 0.61, 0.61, 0.62, 0.63, 0.63, 0.64, 0.64, 0.64 },
{-0.19,-0.14,-0.15,-0.19,-0.27,-0.33,-0.41,-0.46,-0.48,-0.46,-0.42,-0.38,-0.35,-0.31,-0.27,-0.22,-0.15,-0.07, 0.04, 0.18, 0.32, 0.47, 0.60, 0.72, 0.82, 0.90, 0.96, 1.00, 1.02, 1.01, 0.96, 0.88, 0.79, 0.71, 0.66, 0.63, 0.60, 0.55, 0.48, 0.41 },
{-2.73,-2.48,-2.12,-1.70,-1.28,-0.95,-0.71,-0.55,-0.46,-0.41,-0.38,-0.38,-0.38,-0.36,-0.31,-0.24,-0.15,-0.03, 0.10, 0.25, 0.41, 0.58, 0.76, 0.94, 1.14, 1.34, 1.52, 1.66, 1.75, 1.82, 1.92, 2.05, 2.14, 2.21, 2.17, 2.11, 1.95, 1.84, 1.77, 1.77 },
{ 1.44, 1.28, 1.08, 0.86, 0.66, 0.48, 0.32, 0.14,-0.01,-0.11,-0.17,-0.19,-0.20,-0.18,-0.17,-0.15,-0.14,-0.12,-0.08,-0.04, 0.01, 0.06, 0.11, 0.17, 0.21, 0.25, 0.28, 0.30, 0.29, 0.29, 0.26, 0.22, 0.16, 0.09, 0.03,-0.01,-0.03,-0.05,-0.04,-0.02 },
{ 1.36, 1.32, 1.26, 1.18, 1.06, 0.92, 0.75, 0.55, 0.34, 0.15, 0.01,-0.10,-0.16,-0.20,-0.23,-0.25,-0.26,-0.23,-0.18,-0.13,-0.07,-0.01, 0.06, 0.11, 0.16, 0.19, 0.21, 0.23, 0.25, 0.25, 0.24, 0.21, 0.17, 0.13, 0.08, 0.03,-0.03,-0.07,-0.11,-0.14 },
{ 2.92, 2.80, 2.64, 2.39, 2.11, 1.85, 1.69, 1.55, 1.41, 1.23, 1.05, 0.87, 0.71, 0.55, 0.39, 0.23, 0.08,-0.06,-0.18,-0.29,-0.38,-0.45,-0.50,-0.52,-0.52,-0.50,-0.46,-0.41,-0.36,-0.30,-0.26,-0.25,-0.24,-0.22,-0.16,-0.10,-0.04,-0.03,-0.03,-0.05 },
{ 0.67, 0.69, 0.71, 0.73, 0.78, 0.85, 0.93, 0.98, 1.01, 1.00, 0.93, 0.81, 0.64, 0.45, 0.24, 0.07,-0.08,-0.19,-0.30,-0.38,-0.42,-0.43,-0.42,-0.41,-0.37,-0.34,-0.29,-0.24,-0.18,-0.06, 0.08, 0.22, 0.30, 0.34, 0.36, 0.37, 0.39, 0.41, 0.42, 0.43 },
{ 0.01, 0.01, 0.04, 0.11, 0.23, 0.38, 0.51, 0.60, 0.64, 0.62, 0.55, 0.43, 0.29, 0.14, 0.00,-0.11,-0.20,-0.27,-0.30,-0.30,-0.29,-0.27,-0.23,-0.19,-0.14,-0.09,-0.05,-0.01, 0.03, 0.08, 0.12, 0.17, 0.24, 0.32, 0.39, 0.42, 0.41, 0.40, 0.39, 0.38 } }

core::Real envdata[20][40] = { { 0.215, 0.211, 0.199, 0.184, 0.168, 0.155, 0.152, 0.152, 0.156, 0.154, 0.161, 0.187, 0.222, 0.264, 0.290, 0.306, 0.290, 0.254, 0.191, 0.117, 0.037, -0.032, -0.098, -0.162, -0.241, -0.318, -0.393, -0.467, -0.547, -0.634, -0.721, -0.807, -0.894, -0.989, -1.089, -1.179, -1.241, -1.273, -1.282, -1.284 }, {1.947, 1.943, 1.936, 1.933, 1.932, 1.937, 1.934, 1.916, 1.842, 1.699, 1.509, 1.313, 1.124, 0.940, 0.740, 0.561, 0.369, 0.196, 0.008, -0.147, -0.277, -0.371, -0.448, -0.510, -0.567, -0.606, -0.644, -0.669, -0.700, -0.721, -0.734, -0.744, -0.758, -0.810, -0.867, -0.933, -0.976, -1.027, -1.064, -1.088 }, {-0.935, -0.923, -0.892, -0.847, -0.798, -0.752, -0.713, -0.668, -0.620, -0.564, -0.514, -0.466, -0.416, -0.351, -0.272, -0.172, -0.068, 0.043, 0.147, 0.264, 0.391, 0.526, 0.643, 0.741, 0.816, 0.863, 0.884, 0.886, 0.888, 0.900, 0.925, 0.951, 0.972, 0.983, 0.991, 0.997, 1.006, 1.013, 1.016, 1.016 }, {-0.286, -0.309, -0.346, -0.398, -0.442, -0.506, -0.562, -0.624, -0.652, -0.651, -0.620, -0.582, -0.534, -0.469, -0.377, -0.262, -0.129, 0.021, 0.190, 0.372, 0.561, 0.736, 0.907, 1.060, 1.204, 1.310, 1.389, 1.440, 1.473, 1.492, 1.509, 1.540, 1.573, 1.602, 1.615, 1.621, 1.619, 1.618, 1.616, 1.617 }, { 0.760, 0.762, 0.772, 0.798, 0.863, 0.966, 1.085, 1.168, 1.192, 1.167, 1.104, 1.016, 0.896, 0.744, 0.566, 0.361, 0.166, -0.008, -0.149, -0.271, -0.371, -0.441, -0.476, -0.484, -0.470, -0.442, -0.400, -0.349, -0.277, -0.158, 0.009, 0.199, 0.353, 0.450, 0.497, 0.519, 0.533, 0.541, 0.548, 0.551 }, {-0.041, -0.050, -0.056, -0.055, -0.037, -0.028, -0.029, -0.051, -0.076, -0.096, -0.104, -0.106, -0.098, -0.078, -0.040, 0.007, 0.049, 0.080, 0.099, 0.120, 0.134, 0.150, 0.153, 0.150, 0.126, 0.072, -0.006, -0.104, -0.214, -0.341, -0.464, -0.579, -0.678, -0.788, -0.888, -1.000, -1.133, -1.311, -1.489, -1.579 }, { 0.020, 0.018, 0.016, 0.013, 0.018, 0.044, 0.088, 0.140, 0.172, 0.181, 0.166, 0.137, 0.092, 0.033, -0.036, -0.104, -0.151, -0.179, -0.177, -0.159, -0.116, -0.062, -0.007, 0.040, 0.087, 0.128, 0.172, 0.209, 0.242, 0.263, 0.272, 0.277, 0.279, 0.282, 0.280, 0.275, 0.270, 0.271, 0.278, 0.284 }, { 1.167, 1.170, 1.178, 1.193, 1.230, 1.270, 1.315, 1.326, 1.309, 1.247, 1.151, 1.038, 0.899, 0.746, 0.577, 0.407, 0.244, 0.091, -0.041, -0.159, -0.262, -0.362, -0.449, -0.517, -0.551, -0.557, -0.543, -0.514, -0.468, -0.401, -0.331, -0.268, -0.190, -0.082, 0.046, 0.144, 0.200, 0.224, 0.238, 0.244 }, {-0.026, -0.049, -0.092, -0.150, -0.214, -0.289, -0.359, -0.416, -0.456, -0.488, -0.510, -0.519, -0.508, -0.481, -0.438, -0.377, -0.282, -0.154, 0.018, 0.226, 0.454, 0.683, 0.908, 1.122, 1.328, 1.497, 1.638, 1.730, 1.800, 1.870, 1.969, 2.081, 2.168, 2.219, 2.244, 2.260, 2.266, 2.262, 2.254, 2.249 }, { 1.128, 1.132, 1.141, 1.156, 1.178, 1.212, 1.251, 1.270, 1.244, 1.167, 1.060, 0.936, 0.791, 0.624, 0.449, 0.281, 0.131, -0.007, -0.130, -0.242, -0.333, -0.406, -0.452, -0.476, -0.471, -0.444, -0.396, -0.323, -0.229, -0.120, -0.010, 0.108, 0.222, 0.374, 0.552, 0.783, 0.986, 1.139, 1.208, 1.232 }, { 0.756, 0.758, 0.766, 0.784, 0.807, 0.841, 0.874, 0.914, 0.910, 0.867, 0.766, 0.668, 0.557, 0.452, 0.333, 0.230, 0.133, 0.053, -0.028, -0.097, -0.169, -0.238, -0.317, -0.381, -0.423, -0.438, -0.443, -0.434, -0.423, -0.388, -0.387, -0.381, -0.412, -0.418, -0.438, -0.445, -0.454, -0.461, -0.466, -0.471 }, {-0.510, -0.515, -0.528, -0.545, -0.569, -0.579, -0.568, -0.513, -0.457, -0.397, -0.361, -0.322, -0.290, -0.250, -0.206, -0.152, -0.083, -0.006, 0.081, 0.162, 0.246, 0.327, 0.404, 0.462, 0.502, 0.529, 0.548, 0.561, 0.567, 0.576, 0.582, 0.594, 0.606, 0.621, 0.634, 0.645, 0.653, 0.662, 0.670, 0.675 }, {-1.240, -1.229, -1.194, -1.123, -1.022, -0.910, -0.810, -0.720, -0.620, -0.510, -0.394, -0.296, -0.204, -0.126, -0.054, -0.002, 0.042, 0.083, 0.137, 0.191, 0.247, 0.302, 0.359, 0.408, 0.430, 0.431, 0.409, 0.383, 0.354, 0.342, 0.336, 0.335, 0.338, 0.348, 0.360, 0.365, 0.370, 0.375, 0.380, 0.383 }, {-0.072, -0.067, -0.061, -0.055, -0.050, -0.066, -0.103, -0.174, -0.242, -0.309, -0.354, -0.386, -0.390, -0.372, -0.337, -0.284, -0.220, -0.130, -0.028, 0.099, 0.227, 0.361, 0.488, 0.602, 0.704, 0.786, 0.852, 0.898, 0.947, 1.006, 1.083, 1.158, 1.240, 1.335, 1.446, 1.548, 1.633, 1.702, 1.766, 1.796 }, { 0.190, 0.188, 0.183, 0.177, 0.177, 0.173, 0.154, 0.111, 0.047, -0.032, -0.119, -0.200, -0.271, -0.324, -0.358, -0.363, -0.346, -0.297, -0.213, -0.097, 0.039, 0.189, 0.352, 0.519, 0.681, 0.831, 0.982, 1.116, 1.252, 1.380, 1.509, 1.606, 1.668, 1.699, 1.713, 1.719, 1.720, 1.720, 1.720, 1.720 }, {-0.321, -0.323, -0.327, -0.338, -0.351, -0.365, -0.371, -0.367, -0.350, -0.321, -0.283, -0.237, -0.186, -0.129, -0.072, -0.019, 0.030, 0.076, 0.121, 0.163, 0.202, 0.233, 0.252, 0.258, 0.249, 0.224, 0.179, 0.118, 0.056, 0.000, -0.057, -0.112, -0.159, -0.184, -0.196, -0.203, -0.211, -0.216, -0.220, -0.221 }, { 0.073, 0.073, 0.073, 0.073, 0.073, 0.073, 0.066, 0.039, -0.004, -0.058, -0.102, -0.136, -0.149, -0.149, -0.139, -0.121, -0.087, -0.039, 0.020, 0.073, 0.124, 0.164, 0.197, 0.209, 0.199, 0.163, 0.118, 0.066, 0.015, -0.038, -0.083, -0.120, -0.147, -0.167, -0.182, -0.190, -0.197, -0.202, -0.206, -0.208 }, { 1.137, 1.138, 1.138, 1.142, 1.143, 1.148, 1.145, 1.133, 1.094, 1.027, 0.942, 0.838, 0.729, 0.608, 0.489, 0.367, 0.253, 0.143, 0.036, -0.078, -0.183, -0.277, -0.353, -0.422, -0.482, -0.532, -0.569, -0.589, -0.592, -0.588, -0.577, -0.573, -0.567, -0.577, -0.585, -0.599, -0.602, -0.606, -0.605, -0.605 }, { 1.430, 1.430, 1.430, 1.413, 1.374, 1.311, 1.240, 1.182, 1.134, 1.088, 1.022, 0.916, 0.773, 0.597, 0.407, 0.228, 0.051, -0.097, -0.239, -0.340, -0.410, -0.431, -0.428, -0.408, -0.381, -0.336, -0.263, -0.153, -0.014, 0.128, 0.247, 0.357, 0.474, 0.607, 0.729, 0.823, 0.877, 0.902, 0.912, 0.917 }, { 1.037, 1.040, 1.046, 1.051, 1.051, 1.051, 1.050, 1.047, 1.021, 0.973, 0.896, 0.804, 0.684, 0.534, 0.362, 0.182, 0.018, -0.133, -0.254, -0.343, -0.397, -0.422, -0.424, -0.396, -0.343, -0.263, -0.178, -0.068, 0.049, 0.200, 0.367, 0.550, 0.725, 0.874, 0.991, 1.067, 1.115, 1.142, 1.158, 1.165 } };

Referenced by core::scoring::methods::EnvSmoothEnergy::calc_energy().

basic::Tracer core::scoring::methods::GEOMETRIES("core.scoring.CartesianBondedEnergy.GEOMETRIES")
static
const Real core::scoring::methods::K_ANGLE =80.0
static
const Real core::scoring::methods::K_LENGTH =300.0
static
const Real core::scoring::methods::K_TORSION =20.0
static
const Real core::scoring::methods::K_TORSION_IMPROPER =40.0
static
const Real core::scoring::methods::K_TORSION_PROTON =10.0
static
Real const core::scoring::methods::optimal_water_distance(2.65)
static
Distance const core::scoring::methods::start_sig = 9.8
DistanceSquared const core::scoring::methods::start_sig2 = start_sig*start_sig
basic::Tracer core::scoring::methods::tr("core.scoring.methods")
static
basic::Tracer core::scoring::methods::TR("core.scoring.methods.D2H_SA_Energy.cc")
static
basic::Tracer core::scoring::methods::TR("core.scoring.GoapEnergy")
static
basic::Tracer core::scoring::methods::tr("core.scoring.LinearChainbreak", basic::t_info)
static
basic::Tracer core::scoring::methods::TR("core.scoring.methods.MMTorsionEnergy")
static
basic::Tracer core::scoring::methods::tr("core.scoring.methods.CustomAtomPairEnergy")
static
basic::Tracer core::scoring::methods::TR("core.mm.MMBondLengthEnergy")
static
basic::Tracer core::scoring::methods::TR("core.mm.MMBondAngleEnergy")
static
basic::Tracer core::scoring::methods::TR("core.scoring.methods.ProQ_Energy.cc")
static
basic::Tracer core::scoring::methods::TR("core.scoring.Rama2BOffsetEnergy")
static
basic::Tracer core::scoring::methods::TR("core.scoring.methods.LK_BallInfo")
static
basic::Tracer core::scoring::methods::TR("core.scoring.methods.LK_BallEnergy")
static
basic::Tracer core::scoring::methods::TR("core.scoring.CartesianBondedEnergy")
static

Referenced by build_optimal_water_Os_on_acceptor(), core::scoring::methods::D2H_SA_Energy::D2H_SA_Energy(), core::scoring::methods::CartesianBondedEnergy::eval_improper_torsions(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_torsion_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::scoring::methods::D2H_SA_Energy::finalize_total_energy(), core::scoring::methods::ProQ_Energy::finalize_total_energy(), core::scoring::methods::IdealParametersDatabase::init(), core::scoring::methods::ProQ_Energy::initialize(), core::scoring::methods::LKB_ResidueInfo::initialize_residue_type(), core::scoring::methods::IdealParametersDatabase::lookup_angle(), core::scoring::methods::IdealParametersDatabase::lookup_length(), core::scoring::methods::NMerSVMEnergy::read_aa_encoding_matrix(), core::scoring::methods::IdealParametersDatabase::read_angle_database(), core::scoring::methods::GoapEnergy::read_angle_definitions(), core::scoring::methods::IdealParametersDatabase::read_length_database(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm_list(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssms_from_options(), core::scoring::methods::NMerSVMEnergy::read_nmer_svm(), core::scoring::methods::NMerSVMEnergy::read_nmer_svm_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::GoapEnergy::read_potential_values(), core::scoring::methods::ProQ_Energy::read_profiles_and_entropy(), core::scoring::methods::IdealParametersDatabase::read_torsion_database(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::LKB_ResidueInfo::setup_atom_weights(), core::scoring::methods::LK_BallEnergy::setup_d2_bounds(), core::scoring::methods::PoissonBoltzmannEnergy::setup_for_scoring(), core::scoring::methods::GoapEnergy::setup_for_scoring(), core::scoring::methods::CartesianBondedEnergy::setup_for_scoring(), setup_water_builders_for_residue_type(), and core::scoring::methods::UnfoldedStateEnergy::UnfoldedStateEnergy().

Real const core::scoring::methods::vdw_scale_factor(0.8)