Rosetta 3.4
Namespaces | Classes | Typedefs | Enumerations | Functions | Variables
core::scoring::methods Namespace Reference

Namespaces

namespace  dfire

Classes

class  BurialEnergy
class  BurialEnergyCreator
class  TorsionDatabase
class  BondAngleDatabase
class  BondLengthDatabase
class  CartesianBondedEnergy
class  CartesianBondedEnergyCreator
class  CenHBEnergy
class  CenHBEnergyCreator
class  CenPairEnergy
class  CenPairEnergyCreator
class  ChainbreakEnergy
 ChainbreakEnergy 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  ChainbreakEnergyCreator
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  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  GaussianOverlapEnergy
class  GaussianOverlapEnergyCreator
class  GenBornEnergy
class  GenBornEnergyCreator
class  HybridVDW_Energy
class  HybridVDW_EnergyCreator
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  WaterBuilder
class  LKB_ResidueInfo
class  LKB_ResiduesInfo
class  LK_CosThetaEnergy
class  LK_CosThetaEnergyCreator
class  LK_SigmoidalFunc
class  LK_hack
class  LK_hackCreator
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  MMBondAngleEnergy
class  MMBondAngleEnergyCreator
class  MMBondLengthEnergy
class  MMBondLengthEnergyCreator
class  MMLJEnergyInter
class  MMLJEnergyInterCreator
class  MMLJEnergyIntra
class  MMLJEnergyIntraCreator
class  MMTorsionEnergy
class  MMTorsionEnergyCreator
class  OmegaTetherEnergy
class  OmegaTetherEnergyCreator
class  OneBodyEnergy
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  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  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  RamachandranEnergy
class  RamachandranEnergy2B
class  RamachandranEnergy2BCreator
class  RamachandranEnergyCreator
class  ReferenceEnergy
class  ReferenceEnergyCreator
class  ResidualDipolarCouplingEnergy
class  ResidualDipolarCouplingEnergy_Rohl
class  ResidualDipolarCouplingEnergy_RohlCreator
class  ResidualDipolarCouplingEnergyCreator
class  ResidualDipolarCouplingEnergyRigidSegments
class  RG_Energy
class  RG_MinData
class  RG_Energy_Fast
class  RG_Energy_FastCreator
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  VDW_Energy
class  VDW_EnergyCreator
class  WaterAdductHBondEnergy
class  WaterAdductHBondEnergyCreator
class  WaterAdductIntraEnergy
class  WaterAdductIntraEnergyCreator
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::owning_ptr
< TorsionDatabase
TorsionDatabaseOP
typedef
utility::pointer::owning_ptr
< BondAngleDatabase
BondAngleDatabaseOP
typedef
utility::pointer::owning_ptr
< BondLengthDatabase
BondLengthDatabaseOP
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
< 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
< 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::vector1
< WaterBuilder
WaterBuilders
typedef
utility::pointer::owning_ptr
< LKB_ResidueInfo
LKB_ResidueInfoOP
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
< 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
< 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::owning_ptr
< ProClosureEnergy
ProClosureEnergyOP
typedef
utility::pointer::owning_ptr
< ProClosureEnergy const > 
ProClosureEnergyCOP
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
< ResidualDipolarCouplingEnergy
ResidualDipolarCouplingEnergyOP
typedef
utility::pointer::owning_ptr
< ResidualDipolarCouplingEnergyRigidSegments
ResidualDipolarCouplingEnergyRigidSegmentsOP
typedef
utility::pointer::owning_ptr
< RG_MinData
RG_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, hackelec_method,
  mm_lj_energy_inter_method, pair_e_method, reference_e_method, ramachandran_method,
  n_energy_methods = ramachandran_method
}
enum  LongRangeEnergyType {
  constraints_lr = 1, gen_born_lr, PB_elec_lr, cart_bonded_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

static basic::Tracer TR ("core.scoring.CartesianBondedEnergy")
std::string get_restag (core::chemical::ResidueType const &restype)
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 &tree, utility::vector1< int > *cutpoints)
static basic::Tracer tr ("core.scoring.methods.CustomAtomPairEnergy")
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
bool count_pair_bs (Size const pos1, Size const pos2, BasePartner const &partner)
 ordered!!!! requires pos1<pos2
BasePartner const & retrieve_base_partner_from_pose_inline (pose::Pose const &pose)
 same as dna::retrieve_base_partner_from_pose
bool operator== (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
 used inside ScoreFunctionInfo::operator==
bool operator!= (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
 used inside ScoreFunctionInfo::operator==
std::ostream & operator<< (std::ostream &out, EnergyMethodOptions const &options)
Real sqr (Real x)
bool count_atom (int const &atype)
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")
LKB_RotamerSetInfo const & retrieve_rotamer_set_info (conformation::RotamerSetBase const &set)
 inline retrieval functions here:
LKB_ResidueInfo const & retrieve_residue_info (pose::Pose const &pose, Size const seqpos)
LKB_ResidueInforetrieve_nonconst_residue_info (pose::Pose &pose, Size const seqpos)
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
static basic::Tracer TR ("core.scoring.methods.LK_BallInfo")
static Real const optimal_water_distance (2.65)
bool residue_type_has_waters (ResidueType const &rsd_type)
 note that this number is re-defined in hbonds.cc !!
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)
static basic::Tracer TR ("core.mm.MMBondAngleEnergy")
static basic::Tracer TR ("core.mm.MMBondLengthEnergy")
static basic::Tracer TR ("core.scoring.methods.MMTorsionEnergy")
template<class T >
utility::pointer::access_ptr< T > _AP (T &o)
template<class T >
utility::pointer::access_ptr
< T const > 
_CAP (T const &o)
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)

Variables

static const Real K_LENGTH = 300.0
static const Real K_ANGLE = 150.0
static const Real K_TORSION = 100.0
static const Real K_TORSION_PROTON = 30.0
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_coarse [20][40]
core::Real const envdata [20][40]

Typedef Documentation


Enumeration Type Documentation

Enumerator:
etable_method 
dunbrack_method 
hbond_method 
hackelec_method 
mm_lj_energy_inter_method 
pair_e_method 
reference_e_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 
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 
)
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 tree,
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 
)
static Real const core::scoring::methods::optimal_water_distance ( 2.  65) [static]
bool core::scoring::methods::residue_type_has_waters ( ResidueType const &  rsd_type) [inline]
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_ResidueInfo& core::scoring::methods::retrieve_nonconst_residue_info ( pose::Pose pose,
Size const  seqpos 
) [inline]
LKB_ResidueInfo const& core::scoring::methods::retrieve_residue_info ( pose::Pose const &  pose,
Size const  seqpos 
) [inline]
LKB_RotamerSetInfo const& core::scoring::methods::retrieve_rotamer_set_info ( conformation::RotamerSetBase const &  set) [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 
)
static basic::Tracer core::scoring::methods::tr ( "core.scoring.LinearChainbreak"  ,
basic::t_info   
) [static]
static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.LK_BallEnergy"  ) [static]
static basic::Tracer core::scoring::methods::TR ( "core.scoring.CartesianBondedEnergy"  ) [static]
static basic::Tracer core::scoring::methods::TR ( "core.mm.MMBondAngleEnergy"  ) [static]
static basic::Tracer core::scoring::methods::TR ( "core.scoring.methods.LK_BallInfo"  ) [static]
static basic::Tracer core::scoring::methods::tr ( "core.scoring.methods.CustomAtomPairEnergy"  ) [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]
Real const core::scoring::methods::vdw_scale_factor ( 0.  8)

Variable Documentation

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 } }
Initial value:
 {
{ 0.86, 3.30, 3.30, 2.79, 1.75, 0.99, 0.91, 0.60, 0.46, 0.33, 0.19, 0.25, 0.20, 0.22, 0.18, 0.18, 0.12, 0.08,-0.03,-0.07,-0.18,-0.23,-0.26,-0.25,-0.29,-0.29,-0.28,-0.28,-0.29,-0.32,-0.35,-0.45,-0.59,-0.59,-0.74,-1.05,-0.71,-0.79,-0.71,-1.00},
{-0.28, 2.17, 2.17, 2.42, 2.20, 2.35, 1.99, 2.21, 2.12, 1.68, 1.48, 1.39, 1.26, 0.96, 0.84, 0.60, 0.40, 0.17,-0.00,-0.22,-0.37,-0.46,-0.53,-0.57,-0.61,-0.69,-0.69,-0.73,-0.72,-0.84,-0.68,-0.74,-0.67,-0.88,-0.93,-0.41,-1.15,-1.28,-1.28,-1.28},
{-0.50, 2.55, 2.55, 1.09,-0.12,-0.35,-0.42,-0.54,-0.48,-0.54,-0.52,-0.51,-0.42,-0.41,-0.31,-0.22,-0.11,-0.03, 0.12, 0.28, 0.39, 0.59, 0.65, 0.75, 0.93, 1.08, 1.20, 1.15, 1.18, 1.16, 1.07, 1.23, 1.26, 1.41, 1.85, 1.88, 1.02, 1.02, 1.02, 1.02},
{-0.17,-0.03,-0.03,-0.79,-0.83,-0.72,-0.87,-0.82,-0.81,-0.69,-0.65,-0.54,-0.45,-0.35,-0.25,-0.12, 0.07, 0.25, 0.40, 0.54, 0.77, 0.90, 1.10, 1.17, 1.35, 1.43, 1.50, 1.66, 1.72, 1.71, 1.68, 1.80, 1.86, 1.79, 1.53, 2.29, 2.06, 2.06, 1.01, 0.39},
{ 0.83, 0.33, 0.01, 0.05, 0.34, 0.49, 0.77, 0.88, 1.07, 1.10, 1.07, 0.99, 0.89, 0.76, 0.58, 0.45, 0.28, 0.19, 0.10,-0.03,-0.16,-0.27,-0.32,-0.44,-0.53,-0.58,-0.65,-0.74,-0.80,-0.78,-0.74,-0.68,-0.58,-0.32,-0.41,-0.25,-0.39, 0.73, 0.51, 0.51},
{ 0.36, 2.30, 2.30, 3.06, 2.20, 1.23, 0.75, 0.41, 0.19, 0.09, 0.00,-0.11,-0.11,-0.15,-0.16,-0.12,-0.11,-0.11,-0.12,-0.05,-0.07,-0.01, 0.02, 0.04, 0.12, 0.11, 0.09, 0.05, 0.03,-0.09,-0.13,-0.26,-0.33,-0.55,-0.62,-0.80,-0.83,-1.30,-0.94,-1.68},
{-0.42,-0.22,-0.38,-0.72,-0.47,-0.38,-0.18,-0.17,-0.07,-0.03,-0.04,-0.06,-0.15,-0.10,-0.15,-0.19,-0.20,-0.12,-0.01,-0.09, 0.02, 0.07, 0.20, 0.27, 0.34, 0.33, 0.37, 0.36, 0.31, 0.34, 0.23, 0.38, 0.38, 0.37, 0.17, 0.03, 0.60, 0.18, 0.18, 0.18},
{-0.63, 2.00, 2.00, 1.03, 0.94, 1.32, 1.35, 1.50, 1.30, 1.27, 1.06, 1.05, 1.02, 0.87, 0.74, 0.60, 0.48, 0.39, 0.18, 0.09,-0.09,-0.19,-0.28,-0.42,-0.55,-0.65,-0.78,-0.86,-0.97,-1.01,-1.07,-1.05,-1.03,-0.97,-1.02,-0.90,-0.84,-0.72,-0.76,-0.47},
{ 0.09,-0.92,-1.60,-1.63,-1.51,-1.35,-1.24,-1.07,-0.87,-0.70,-0.59,-0.50,-0.41,-0.29,-0.17, 0.01, 0.21, 0.44, 0.63, 0.87, 1.18, 1.31, 1.51, 1.75, 1.89, 2.04, 2.20, 2.14, 2.20, 2.22, 2.24, 1.96, 2.04, 2.29, 2.42, 2.14, 2.61, 2.61, 2.61, 2.61},
{ 0.38, 3.38, 3.38, 2.13, 1.48, 1.56, 1.44, 1.52, 1.28, 1.13, 1.10, 1.05, 0.85, 0.69, 0.50, 0.30, 0.15,-0.04,-0.12,-0.26,-0.30,-0.40,-0.51,-0.57,-0.61,-0.62,-0.60,-0.54,-0.43,-0.38,-0.26,-0.18,-0.09, 0.06, 0.41, 0.60, 0.01, 0.84, 0.62, 0.62},
{ 0.04, 0.24, 0.69, 0.58, 0.65, 0.52, 0.75, 0.75, 0.73, 0.80, 0.84, 0.80, 0.88, 0.61, 0.52, 0.40, 0.30, 0.18, 0.12, 0.03,-0.11,-0.14,-0.22,-0.34,-0.42,-0.52,-0.62,-0.68,-0.80,-0.85,-0.96,-0.90,-0.91,-0.89,-0.70,-0.79,-0.33,-0.46,-0.28,-0.28},
{ 0.48, 1.95, 1.95, 1.05,-0.21,-0.34,-0.35,-0.33,-0.33,-0.40,-0.34,-0.30,-0.31,-0.27,-0.21,-0.17,-0.14,-0.12, 0.00, 0.08, 0.16, 0.25, 0.38, 0.53, 0.60, 0.61, 0.75, 0.79, 0.78, 0.71, 0.71, 0.72, 0.85, 0.96, 1.09, 0.65, 0.93, 0.93, 0.57, 0.57},
{ 0.96, 2.02, 2.02, 1.58, 0.24,-0.18,-0.37,-0.46,-0.36,-0.33,-0.26,-0.20,-0.18,-0.13,-0.10,-0.11,-0.07,-0.04,-0.00,-0.00, 0.08, 0.14, 0.23, 0.27, 0.42, 0.45, 0.43, 0.48, 0.55, 0.63, 0.62, 0.55, 0.56, 0.73, 0.44, 0.54, 0.78, 0.87, 0.64, 0.64},
{-0.19, 0.46, 0.46,-0.20,-0.30,-0.25,-0.49,-0.45,-0.51,-0.50,-0.41,-0.36,-0.36,-0.33,-0.27,-0.21,-0.18,-0.09, 0.04, 0.16, 0.32, 0.51, 0.58, 0.73, 0.89, 0.86, 0.98, 1.06, 0.97, 1.06, 1.02, 0.86, 0.80, 0.65, 0.93, 1.40, 2.15, 0.63, 0.41, 0.41},
{-0.67,-2.65,-2.20,-1.66,-1.17,-0.94,-0.63,-0.49,-0.44,-0.42,-0.34,-0.37,-0.41,-0.39,-0.31,-0.25,-0.19,-0.01, 0.07, 0.25, 0.40, 0.59, 0.76, 0.90, 1.16, 1.34, 1.54, 1.70, 1.84, 1.75, 1.82, 2.14, 2.21, 2.24, 2.09, 2.41, 1.77, 1.77, 1.77, 1.77},
{-0.06, 1.39, 2.54, 2.80, 1.26, 0.45, 0.39, 0.11,-0.08,-0.12,-0.19,-0.22,-0.21,-0.17,-0.17,-0.15,-0.14,-0.12,-0.11,-0.03, 0.02, 0.04, 0.11, 0.21, 0.17, 0.26, 0.31, 0.30, 0.29, 0.33, 0.21, 0.28, 0.18, 0.06,-0.07, 0.31,-0.02,-0.40,-0.92, 0.25},
{-0.47, 2.89, 2.89, 2.86, 1.39, 0.90, 0.82, 0.57, 0.28, 0.11, 0.01,-0.14,-0.19,-0.19,-0.24,-0.27,-0.28,-0.25,-0.18,-0.13,-0.08,-0.03, 0.09, 0.10, 0.17, 0.22, 0.20, 0.21, 0.29, 0.24, 0.25, 0.23, 0.18, 0.10, 0.43, 0.36,-0.07,-0.05,-0.28, 0.20},
{-0.09, 3.86, 3.86, 4.12, 2.10, 1.67, 1.69, 1.62, 1.44, 1.20, 1.05, 0.85, 0.73, 0.54, 0.40, 0.22, 0.05,-0.06,-0.17,-0.32,-0.38,-0.47,-0.52,-0.52,-0.54,-0.50,-0.47,-0.42,-0.36,-0.28,-0.25,-0.26,-0.17,-0.33,-0.18, 0.11, 0.01,-0.06,-0.00,-0.62},
{-0.00,-0.00, 1.55, 0.42, 0.76, 0.85, 0.96, 0.97, 1.05, 1.05, 0.95, 0.87, 0.65, 0.47, 0.19, 0.05,-0.09,-0.19,-0.32,-0.41,-0.47,-0.41,-0.41,-0.46,-0.34,-0.36,-0.29,-0.22,-0.25,-0.10, 0.10, 0.28, 0.39, 0.66, 0.34, 1.86, 1.86, 1.86, 1.86, 1.86},
{ 1.40,-0.20, 0.01,-0.29, 0.24, 0.38, 0.55, 0.63, 0.70, 0.65, 0.58, 0.44, 0.30, 0.12,-0.01,-0.15,-0.18,-0.31,-0.33,-0.31,-0.28,-0.28,-0.26,-0.16,-0.14,-0.11,-0.05, 0.02,-0.02, 0.11, 0.16, 0.12, 0.17, 0.38, 0.45, 0.12, 0.74, 0.74, 0.38, 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 } };

const Real core::scoring::methods::K_ANGLE = 150.0 [static]
const Real core::scoring::methods::K_LENGTH = 300.0 [static]
const Real core::scoring::methods::K_TORSION = 100.0 [static]
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