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core::scoring::etable::Etable Class Reference

Class definition for Etable. More...

#include <Etable.hh>

Inheritance diagram for core::scoring::etable::Etable:
Inheritance graph
[legend]

Public Member Functions

 ~Etable () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
 Etable (chemical::AtomTypeSetCAP atom_set_in, EtableOptions const &options, std::string const &alternate_parameter_set="")
 constructor More...
 
int n_atomtypes () const
 
Real Wradius () const
 
Real lj_switch_dis2sigma () const
 
Real etable_disbins () const
 
bool lj_use_lj_deriv_slope () const
 
Real lj_slope_intercept () const
 
bool lj_use_hbond_radii () const
 
bool lj_use_water_radii () const
 
Real lj_water_dis () const
 
Real lj_water_hdis () const
 
Real lk_min_dis2sigma () const
 
Real min_dis () const
 
Real min_dis2 () const
 
bool add_long_range_damping () const
 
Real long_range_damping_length () const
 
Real epsilon () const
 
ObjexxFCL::FArray3D< Real > const & ljatr () const
 const access to the arrays More...
 
ObjexxFCL::FArray3D< Real > const & ljrep () const
 
virtual ObjexxFCL::FArray3D
< Real > const & 
solv1 () const
 
virtual ObjexxFCL::FArray3D
< Real > const & 
solv2 () const
 
ObjexxFCL::FArray3D< Real > const & dljatr () const
 const access to the deriv arrays More...
 
ObjexxFCL::FArray3D< Real > const & dljrep () const
 
virtual ObjexxFCL::FArray3D
< Real > const & 
dsolv1 () const
 return the solvation derivative table for the desolvation of atom1 by atom2 More...
 
ObjexxFCL::FArray3D< Real > const & dsolv () const
 return the solvation derivative table that combines atom1 and atom2's desolvations More...
 
Real max_dis () const
 
Real max_dis2 () const
 
Real get_safe_max_dis2 () const
 
int get_bins_per_A2 () const
 
chemical::AtomTypeSetCAP atom_set () const
 
bool fa_hatr () const
 Do hydrogens provide attractive forces or do they only repell? More...
 
Real hydrogen_interaction_cutoff2 () const
 
Real max_heavy_heavy_cutoff () const
 
Real max_heavy_hydrogen_cutoff () const
 
Real max_hydrogen_hydrogen_cutoff () const
 
virtual Real nblist_dis2_cutoff_XX () const
 The square distance cutoff beyond which any pair of heavy-atoms is guaranteed to have an interaction energy of zero. This function is used by the NeighborList. More...
 
virtual Real nblist_dis2_cutoff_XH () const
 The square distance cutoff beyond which a hydrogen/heavy-atom pair is guaranteed to have an interaction energy of zero. This function is used by the NeighborList. More...
 
virtual Real nblist_dis2_cutoff_HH () const
 The square distance cutoff beyond which any hydrogen/hydrogen pair is guaranteed to have an interaction energy of zero. This function is used by the NeighborList. More...
 
Real max_non_hydrogen_lj_radius () const
 Returns the maximum lj radius for any non-hydrogen atom as defined by the atom-type-set used to create this Etable. More...
 
Real max_hydrogen_lj_radius () const
 Returns the maximum lj radius for any hydrogen atom as defined by the input atom-type-set used to create this Etable. More...
 
virtual Real lj_radius (int const i) const
 Return the Lennard-Jones radius for an atom. More...
 
Real lj_wdepth (int const i) const
 Return the Lennard-Jones well depth for an atom. More...
 
virtual Real lk_dgfree (int const i) const
 Return the Lazardis Karplus DGFree value for an atom. More...
 
virtual Real lk_volume (int const i) const
 Return the Lazaridis Karplus volume for an atom. More...
 
virtual Real lk_lambda (int const i) const
 Return the Lazaridis Karplus "lambda" value (correlation distance) for an atom. More...
 
Real lk_inv_lambda2 (int const i) const
 
chemical::AtomType const & atom_type (int const type)
 
Real fasol_cubic_poly_far_xlo () const
 
Real fasol_cubic_poly_far_xhi () const
 
void interpolated_analytic_etable_evaluation (conformation::Atom const &at1, conformation::Atom const &at2, Real &lj_atrE, Real &lj_repE, Real &fa_solE, Real &d2) const
 Use the analytic_etable_evaluation function to evaluate the energy of two atoms, but evaluate the function at the old grid points and then interpolate between them the way the existing etable does (in square distance space). Useful for comparing the original etable evaluation with the analytic evaluation. More...
 
void analytic_etable_evaluation (conformation::Atom const &at1, conformation::Atom const &at2, Real &lj_atrE, Real &lj_repE, Real &fa_solE, Real &d2) const
 Use an analytic functional form of the etable to evaluate an atom-pair energy without reading from the enormous and uncachable tables. More...
 
void analytic_lk_energy (conformation::Atom const &at1, conformation::Atom const &at2, Real &fa_solE1, Real &fa_solE2) const
 Use an analytic functional form of the etable to evaluate only the LK atom-pair energy computing the desolvation of atom1 by atom2 separately from the desolvation of atom2 by atom1. More...
 
void analytic_etable_derivatives (conformation::Atom const &at1, conformation::Atom const &at2, Real &dljatrE_ddis, Real &dljrepE_ddis, Real &dfasolE_ddis, Real &inv_d) const
 Analytically evaluate the energy derivatives for a pair of atoms. More...
 
void analytic_lk_derivatives (conformation::Atom const &at1, conformation::Atom const &at2, Real &dfasolE1_ddis, Real &dfasolE2_ddis, Real &inv_d) const
 Analytically evaluate the LK solvation derivatives for a pair of atoms, separately computing the derivative for atom2's desolvation of atom1 (dfasolE1_ddis) and atom1's desolvation of atom2 (dfasolE2_ddis). More...
 
EtableParamsOnePair const & analytic_params_for_pair (Size atype1, Size atype2) const
 
virtual void output_etable (ObjexxFCL::FArray3D< Real > &etable, std::string label, std::ostream &out)
 output an etable data file in the same format used in input_etable More...
 
virtual void input_etable (ObjexxFCL::FArray3D< Real > &etable, std::string const &label, std::istream &in)
 read in etable from a datafile More...
 
Real get_lj_hbond_OH_donor_dis () const
 
Real get_lj_hbond_hdis () const
 
Real get_lj_hbond_dis () const
 

Private Member Functions

void dimension_etable_arrays ()
 Use an analytic functional form of the etable to evaluate an atom-pair energy without reading from the enormous and uncachable tables. This version is reserved for interactions with hydrogens (hydorgen/hydrogen and hydrogen heavyatom) More...
 
void initialize_from_input_atomset (chemical::AtomTypeSetCAP atom_set_in)
 
void calculate_nblist_distance_thresholds (EtableOptions const &options)
 
void read_alternate_parameter_set (chemical::AtomTypeSetCAP atom_set_in, std::string const &alternate_parameter_set)
 
void calculate_hydrogen_atom_reach ()
 
void initialize_carbontypes_to_linearize_fasol ()
 
Real analytic_ljrep_linearized (Real const dis, EtableParamsOnePair const &p) const
 
Real analytic_lj_generic_form (Real const dis2, Real const inv_dis2, EtableParamsOnePair const &p) const
 
Real analytic_ljatr_cubic_poly_ramp_to_zero (Real const dis, EtableParamsOnePair const &p) const
 
Real analytic_ljatr_cubic_poly_ramp_to_zero_deriv (Real const dis, EtableParamsOnePair const &p) const
 
void analytic_lk_evaluation (int const atype1, int const atype2, EtableParamsOnePair const &p, Real const dis, Real const inv_dis2, Real &fa_solE) const
 Evaluate the mututal desolvation energy as atom 1 and atom 2 approach. Combine the desolvation of atom 1 by atom 2 into the same value as the desolvation of atom 2 by atom 1. More...
 
void analytic_lk_evaluation_individual (int const atype1, int const atype2, EtableParamsOnePair const &p, Real const dis, Real const inv_dis2, Real &fa_solE1, Real &fa_solE2) const
 Evaluate the LK solvation energy for a pair of atoms individually; fa_solE1 returns the desolvation of atom 1 by atom 2 and fa_solE2 returns the desolvation of atom 2 by atom 1. More...
 
EtableParamsOnePairanalytic_params_for_pair (Size atype1, Size atype2)
 
void make_pairenergy_table ()
 calculate fast lookup arrays for vdw and solvation energy More...
 
int calculate_normal_disbins () const
 
void damp_long_range (int const normal_disbins, ObjexxFCL::FArray1A< Real > ljatr, ObjexxFCL::FArray1A< Real > dljatr, ObjexxFCL::FArray1A< Real > ljrep, ObjexxFCL::FArray1A< Real > dljrep, ObjexxFCL::FArray1A< Real > fasol1, ObjexxFCL::FArray1A< Real > fasol2, ObjexxFCL::FArray1A< Real > dfasol, ObjexxFCL::FArray1A< Real > dfasol1)
 
void modify_pot_one_pair (Size atype1, Size atype2, ObjexxFCL::FArray1A< Real > ljatr, ObjexxFCL::FArray1A< Real > dljatr, ObjexxFCL::FArray1A< Real > ljrep, ObjexxFCL::FArray1A< Real > dljrep, ObjexxFCL::FArray1A< Real > fasol1, ObjexxFCL::FArray1A< Real > fasol2, ObjexxFCL::FArray1A< Real > dfasol, ObjexxFCL::FArray1A< Real > dfasol1)
 modify Etable to better treat 0-0, C-C, and H-H interactions More...
 
void assign_parameters_to_full_etables (Size atype1, Size atype2, ObjexxFCL::FArray1A< Real > ljatr, ObjexxFCL::FArray1A< Real > dljatr, ObjexxFCL::FArray1A< Real > ljrep, ObjexxFCL::FArray1A< Real > dljrep, ObjexxFCL::FArray1A< Real > fasol1, ObjexxFCL::FArray1A< Real > fasol2, ObjexxFCL::FArray1A< Real > dfasol, ObjexxFCL::FArray1A< Real > dfasol1)
 
void smooth_etables_one_pair (Size atype1, Size atype2, ObjexxFCL::FArray1A< Real > ljatr, ObjexxFCL::FArray1A< Real > dljatr, ObjexxFCL::FArray1A< Real > ljrep, ObjexxFCL::FArray1A< Real > dljrep, ObjexxFCL::FArray1A< Real > fasol1, ObjexxFCL::FArray1A< Real > fasol2, ObjexxFCL::FArray1A< Real > dfasol, ObjexxFCL::FArray1A< Real > dfasol1)
 
void zero_hydrogen_and_water_ljatr_one_pair (Size atype1, Size atype2, ObjexxFCL::FArray1A< Real > ljrep, ObjexxFCL::FArray1A< Real > ljatr, ObjexxFCL::FArray1A< Real > dljatr, ObjexxFCL::FArray1A< Real > fasol1, ObjexxFCL::FArray1A< Real > fasol2, ObjexxFCL::FArray1A< Real > dfasol, ObjexxFCL::FArray1A< Real > dfasol1)
 
void precalc_etable_coefficients (ObjexxFCL::FArray2< Real > &lj_sigma, ObjexxFCL::FArray2< Real > &lj_r6_coeff, ObjexxFCL::FArray2< Real > &lj_r12_coeff, ObjexxFCL::FArray2< Real > &lj_switch_intercept, ObjexxFCL::FArray2< Real > &lj_switch_slope, ObjexxFCL::FArray1< Real > &lk_inv_lambda2, ObjexxFCL::FArray2< Real > &lk_coeff, ObjexxFCL::FArray2< Real > &lk_min_dis2sigma_value)
 precalculate non-distance dependent coefficients of energy functions More...
 
void calc_etable_value (Real dis2, int atype1, int atype2, Real &atrE, Real &d_atrE, Real &repE, Real &d_repE, Real &solvE1, Real &solvE2, Real &dsolvE1, Real &dsolvE2) const
 calc all etable values given a distance and atom-type pair More...
 
void lk_solv_energy_and_deriv (int atype1, int atype2, Real dis, Real &solvE1, Real &solvE2, Real &dsolvE1, Real &dsolvE2) const
 Analyticaly calculate the Lazaridis-Karplus solvation energy and derivatives for a pair of atoms at a given distance. More...
 

Private Attributes

chemical::AtomTypeSetCAP atom_set_
 
int const n_atomtypes_
 
Real const max_dis_
 
int const bins_per_A2_
 
Real const Wradius_
 
Real const lj_switch_dis2sigma_
 
Real const max_dis2_
 
int const etable_disbins_
 
Real const lj_hbond_OH_donor_dis_
 
Real const lj_hbond_dis_
 
bool const lj_use_lj_deriv_slope_
 
Real const lj_slope_intercept_
 
bool const lj_use_hbond_radii_
 
Real const lj_hbond_hdis_
 
bool const lj_use_water_radii_
 
Real const lj_water_dis_
 
Real const lj_water_hdis_
 
bool const enlarge_h_lj_wdepth_
 
Real const lk_min_dis2sigma_
 
bool const no_lk_polar_desolvation_
 
bool const proline_N_is_lk_nonpolar_
 
Real const min_dis_
 
Real const min_dis2_
 
bool const add_long_range_damping_
 
Real const long_range_damping_length_
 
Real const epsilon_
 
Real const safe_max_dis2_
 
Real hydrogen_interaction_cutoff2_
 
Real max_heavy_hydrogen_cutoff_
 
Real max_hydrogen_hydrogen_cutoff_
 
Real nblist_dis2_cutoff_XX_
 
Real nblist_dis2_cutoff_XH_
 
Real nblist_dis2_cutoff_HH_
 
Real max_non_hydrogen_lj_radius_
 
Real max_hydrogen_lj_radius_
 
bool fa_hatr_
 
Real lj_switch_sigma2dis_
 
Real lj_switch_value2wdepth_
 
Real lj_switch_slope_sigma2wdepth_
 
ObjexxFCL::FArray2D< Reallj_sigma_
 
ObjexxFCL::FArray2D< Reallj_r6_coeff_
 
ObjexxFCL::FArray2D< Reallj_r12_coeff_
 
ObjexxFCL::FArray2D< Reallj_switch_intercept_
 
ObjexxFCL::FArray2D< Reallj_switch_slope_
 
ObjexxFCL::FArray1D< Reallk_inv_lambda2_
 
ObjexxFCL::FArray2D< Reallk_coeff_
 
ObjexxFCL::FArray2D< Reallk_min_dis2sigma_value_
 
Real fasol_cubic_poly_far_xlo_
 
Real fasol_cubic_poly_far_xhi_
 
utility::vector1< Reallj_radius_
 
utility::vector1< Reallj_wdepth_
 
utility::vector1< Reallk_dgfree_
 
utility::vector1< Reallk_volume_
 
utility::vector1< Reallk_lambda_
 
ObjexxFCL::FArray3D< Realljatr_
 
ObjexxFCL::FArray3D< Realljrep_
 
ObjexxFCL::FArray3D< Realsolv1_
 
ObjexxFCL::FArray3D< Realsolv2_
 
ObjexxFCL::FArray3D< Realdljatr_
 
ObjexxFCL::FArray3D< Realdljrep_
 
ObjexxFCL::FArray3D< Realdsolv_
 
ObjexxFCL::FArray3D< Realdsolv1_
 
utility::vector1< Sizecarbon_types_
 
utility::vector1
< EtableParamsOnePair
analytic_parameters_
 
bool slim_
 

Detailed Description

Class definition for Etable.

Constructor & Destructor Documentation

core::scoring::etable::Etable::~Etable ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

core::scoring::etable::Etable::Etable ( chemical::AtomTypeSetCAP  atom_set_in,
EtableOptions const &  options,
std::string const &  alternate_parameter_set = "" 
)

constructor

Note from rhiju & andrew leaver-day: we should get rid of command-line option calls here in favor of setting options from EtableOptions object. Would allow user to have multiple etables around!

References calculate_hydrogen_atom_reach(), calculate_nblist_distance_thresholds(), dimension_etable_arrays(), initialize_carbontypes_to_linearize_fasol(), initialize_from_input_atomset(), make_pairenergy_table(), and read_alternate_parameter_set().

Member Function Documentation

bool core::scoring::etable::Etable::add_long_range_damping ( ) const
inline
void core::scoring::etable::Etable::analytic_etable_derivatives ( conformation::Atom const &  at1,
conformation::Atom const &  at2,
Real dljatrE_ddis,
Real dljrepE_ddis,
Real dfasolE_ddis,
Real inv_d 
) const
inline
void core::scoring::etable::Etable::analytic_etable_evaluation ( conformation::Atom const &  at1,
conformation::Atom const &  at2,
Real lj_atrE,
Real lj_repE,
Real fa_solE,
Real d2 
) const
inline
Real core::scoring::etable::Etable::analytic_lj_generic_form ( Real const  dis2,
Real const  inv_dis2,
EtableParamsOnePair const &  p 
) const
inlineprivate

: evaluate the standard Lennard-Jones 6-12 functional form. Only call this function if the square distance is in the range sqrt( p.ljrep_linear_ramp_d2_cutoff ) < dis < p.ljatr_cubic_poly_xhi

References core::scoring::etable::EtableParamsOnePair::lj_r12_coeff, core::scoring::etable::EtableParamsOnePair::lj_r6_coeff, core::scoring::etable::EtableParamsOnePair::ljatr_cubic_poly_xhi, and core::scoring::etable::EtableParamsOnePair::ljrep_linear_ramp_d2_cutoff.

Referenced by analytic_etable_evaluation().

Real core::scoring::etable::Etable::analytic_ljatr_cubic_poly_ramp_to_zero ( Real const  dis,
EtableParamsOnePair const &  p 
) const
inlineprivate

: evaluate the attractive component of the LJ term as it ramps to zero. Only call this function if the square distance is in the range p.ljatr_cubic_poly_xlo < dis < p.ljatr_cubic_poly_xhi

References core::scoring::etable::EtableParamsOnePair::ljatr_cubic_poly_parameters, core::scoring::etable::EtableParamsOnePair::ljatr_cubic_poly_xhi, and core::scoring::etable::EtableParamsOnePair::ljatr_cubic_poly_xlo.

Referenced by analytic_etable_evaluation().

Real core::scoring::etable::Etable::analytic_ljatr_cubic_poly_ramp_to_zero_deriv ( Real const  dis,
EtableParamsOnePair const &  p 
) const
inlineprivate

: evaluate the derivative for the attractive component of the LJ term as it ramps to zero. Only call this function if the square distance is in the range p.ljatr_cubic_poly_xlo < dis < p.ljatr_cubic_poly_xhi

References core::scoring::etable::EtableParamsOnePair::ljatr_cubic_poly_parameters, core::scoring::etable::EtableParamsOnePair::ljatr_cubic_poly_xhi, and core::scoring::etable::EtableParamsOnePair::ljatr_cubic_poly_xlo.

Referenced by analytic_etable_derivatives().

Real core::scoring::etable::Etable::analytic_ljrep_linearized ( Real const  dis,
EtableParamsOnePair const &  p 
) const
inlineprivate
void core::scoring::etable::Etable::analytic_lk_derivatives ( conformation::Atom const &  at1,
conformation::Atom const &  at2,
Real dfasolE1_ddis,
Real dfasolE2_ddis,
Real inv_d 
) const
inline

Analytically evaluate the LK solvation derivatives for a pair of atoms, separately computing the derivative for atom2's desolvation of atom1 (dfasolE1_ddis) and atom1's desolvation of atom2 (dfasolE2_ddis).

References analytic_params_for_pair(), epsilon_, fasol_cubic_poly_far_xhi_, fasol_cubic_poly_far_xlo_, lj_radius(), lk_inv_lambda2_, max_dis2_, min_dis2_, core::conformation::Atom::type(), and core::conformation::Atom::xyz().

Referenced by core::scoring::etable::AnalyticEtableEvaluator::atom_pair_lk_energy_and_deriv_v(), and core::scoring::etable::AnalyticEtableEvaluator::atom_pair_lk_energy_and_deriv_v_efficient().

void core::scoring::etable::Etable::analytic_lk_energy ( conformation::Atom const &  at1,
conformation::Atom const &  at2,
Real fa_solE1,
Real fa_solE2 
) const
inline
void core::scoring::etable::Etable::analytic_lk_evaluation ( int const  atype1,
int const  atype2,
EtableParamsOnePair const &  p,
Real const  dis,
Real const  inv_dis2,
Real fa_solE 
) const
inlineprivate
void core::scoring::etable::Etable::analytic_lk_evaluation_individual ( int const  atype1,
int const  atype2,
EtableParamsOnePair const &  p,
Real const  dis,
Real const  inv_dis2,
Real fa_solE1,
Real fa_solE2 
) const
inlineprivate
EtableParamsOnePair const & core::scoring::etable::Etable::analytic_params_for_pair ( Size  atype1,
Size  atype2 
) const
inline
EtableParamsOnePair & core::scoring::etable::Etable::analytic_params_for_pair ( Size  atype1,
Size  atype2 
)
inlineprivate
void core::scoring::etable::Etable::assign_parameters_to_full_etables ( Size  atype1,
Size  atype2,
ObjexxFCL::FArray1A< Real ljatr,
ObjexxFCL::FArray1A< Real dljatr,
ObjexxFCL::FArray1A< Real ljrep,
ObjexxFCL::FArray1A< Real dljrep,
ObjexxFCL::FArray1A< Real fasol1,
ObjexxFCL::FArray1A< Real fasol2,
ObjexxFCL::FArray1A< Real dfasol,
ObjexxFCL::FArray1A< Real dfasol1 
)
private
chemical::AtomTypeSetCAP core::scoring::etable::Etable::atom_set ( ) const
inline
chemical::AtomType const& core::scoring::etable::Etable::atom_type ( int const  type)
inline
void core::scoring::etable::Etable::calc_etable_value ( Real  dis2,
int  atype1,
int  atype2,
Real atrE,
Real d_atrE,
Real repE,
Real d_repE,
Real solvE1,
Real solvE2,
Real dsolvE1,
Real dsolvE2 
) const
private

calc all etable values given a distance and atom-type pair

given a pair of atom types and the squared inter-atomic separation distance (and a whole bunch of pre-computed coeffecients), this returns the value of the lennard-jones and lk solvation potentials and their derivatives w.r.t. the separation distance

Parameters
[in]dis2- in - atomic separation distance squared
[in]atype1- in - chemical type of atom 1
[in]atype2- in - chemical type of atom 2
[out]atrE- out - atractive lj energy
[out]d_atrE- out - d(atrE)/d(dis)
[out]repE- out - repulsive lj energy
[out]d_repE- out - d(repE)/d(dis)
[out]solvE1- out - lk solvation energy
[out]solvE2- out - lk solvation energy
[out]dsolvE- out - d(solvE1+solvE2)/d(dis)
[in]lj_sigma- in - for atomtypes i and j: (radius_i+radius_j)
[in]lj_r6_coeff- in - precalced coefficient on the (1/dis)**6 term in lj
[in]lj_r12_coeff- in - precalced coefficient on the (1/dis)**12 term in lj
[in]lj_switch_intercept- in - for close contacts calculate lj from a line with this intercept
[in]lj_switch_slope- in - for close contacts calculate lj from a line with this slope
[in]lk_inv_lambda2- in - surprise! it's the 1/(lambda)**2 term in the lk equation
[in]lk_coeff- in - precalculation of all non-distance dependent terms outside of the exponential in the lk equation
[in]lk_min_dis2sigma_value- in - below the min dis2sigma ratio for lk, this value is assigned to the solvation
Global Read:

pdbstatistics_pack.h etable.h

Global Write:
Remarks
References:
Author
ctsa 10-2003

References epsilon_, lj_r12_coeff_, lj_r6_coeff_, lj_sigma_, lj_switch_dis2sigma_, lj_switch_intercept_, lj_switch_slope_, lk_min_dis2sigma_, lk_min_dis2sigma_value_, lk_solv_energy_and_deriv(), max_dis2_, and min_dis2_.

Referenced by make_pairenergy_table().

void core::scoring::etable::Etable::calculate_hydrogen_atom_reach ( )
private
void core::scoring::etable::Etable::calculate_nblist_distance_thresholds ( EtableOptions const &  options)
private
int core::scoring::etable::Etable::calculate_normal_disbins ( ) const
private
void core::scoring::etable::Etable::damp_long_range ( int const  normal_disbins,
ObjexxFCL::FArray1A< Real ljatr,
ObjexxFCL::FArray1A< Real dljatr,
ObjexxFCL::FArray1A< Real ljrep,
ObjexxFCL::FArray1A< Real dljrep,
ObjexxFCL::FArray1A< Real fasol1,
ObjexxFCL::FArray1A< Real fasol2,
ObjexxFCL::FArray1A< Real dfasol,
ObjexxFCL::FArray1A< Real dfasol1 
)
private
void core::scoring::etable::Etable::dimension_etable_arrays ( )
private

Use an analytic functional form of the etable to evaluate an atom-pair energy without reading from the enormous and uncachable tables. This version is reserved for interactions with hydrogens (hydorgen/hydrogen and hydrogen heavyatom)

References analytic_parameters_, dljatr_, dljrep_, dsolv1_, dsolv_, etable_disbins_, lj_r12_coeff_, lj_r6_coeff_, lj_radius_, lj_sigma_, lj_switch_intercept_, lj_switch_slope_, lj_wdepth_, ljatr_, ljrep_, lk_coeff_, lk_dgfree_, lk_inv_lambda2_, lk_lambda_, lk_min_dis2sigma_value_, lk_volume_, n_atomtypes_, slim_, solv1_, and solv2_.

Referenced by Etable().

ObjexxFCL::FArray3D< Real > const& core::scoring::etable::Etable::dljatr ( ) const
inline
ObjexxFCL::FArray3D< Real > const& core::scoring::etable::Etable::dljrep ( ) const
inline
ObjexxFCL::FArray3D< Real > const& core::scoring::etable::Etable::dsolv ( ) const
inline

return the solvation derivative table that combines atom1 and atom2's desolvations

References dsolv_.

virtual ObjexxFCL::FArray3D< Real > const& core::scoring::etable::Etable::dsolv1 ( ) const
inlinevirtual

return the solvation derivative table for the desolvation of atom1 by atom2

Reimplemented in core::scoring::etable::MembEtable.

References dsolv1_.

Real core::scoring::etable::Etable::epsilon ( ) const
inline
Real core::scoring::etable::Etable::etable_disbins ( ) const
inline
bool core::scoring::etable::Etable::fa_hatr ( ) const
inline

Do hydrogens provide attractive forces or do they only repell?

References fa_hatr_.

Real core::scoring::etable::Etable::fasol_cubic_poly_far_xhi ( ) const
inline
Real core::scoring::etable::Etable::fasol_cubic_poly_far_xlo ( ) const
inline
int core::scoring::etable::Etable::get_bins_per_A2 ( ) const
inline
Real core::scoring::etable::Etable::get_lj_hbond_dis ( ) const
inline
Real core::scoring::etable::Etable::get_lj_hbond_hdis ( ) const
inline
Real core::scoring::etable::Etable::get_lj_hbond_OH_donor_dis ( ) const
inline
Real core::scoring::etable::Etable::get_safe_max_dis2 ( ) const
inline

References safe_max_dis2_.

Real core::scoring::etable::Etable::hydrogen_interaction_cutoff2 ( ) const
inline
void core::scoring::etable::Etable::initialize_carbontypes_to_linearize_fasol ( )
private

References atom_set(), atom_set_, and carbon_types_.

Referenced by Etable().

void core::scoring::etable::Etable::initialize_from_input_atomset ( chemical::AtomTypeSetCAP  atom_set_in)
private
void core::scoring::etable::Etable::input_etable ( ObjexxFCL::FArray3D< Real > &  etable,
std::string const &  label,
std::istream &  in 
)
virtual

read in etable from a datafile

$$$ file first line is <etable> <etable_disbins_> $$$ other lines are <atom type 1> <atomtype 1> <eval bin 1> <eval bin 2>...

Global Read:
pdbstatistics_pack.h: ljatr, dljatr, ljrep, dljrep, solv1,solv2,dsolv
Global Write:
pdbstatistics_pack.h: ljatr, dljatr, ljrep, dljrep, solv1,solv2,dsolv
Remarks
References:
Author
sheffler mar 19 2006

Reimplemented in core::scoring::etable::MembEtable.

References etable_disbins_, and core::scoring::etable::TR().

Referenced by make_pairenergy_table().

void core::scoring::etable::Etable::interpolated_analytic_etable_evaluation ( conformation::Atom const &  at1,
conformation::Atom const &  at2,
core::Real lj_atrE,
core::Real lj_repE,
core::Real fa_solE,
Real d2 
) const

Use the analytic_etable_evaluation function to evaluate the energy of two atoms, but evaluate the function at the old grid points and then interpolate between them the way the existing etable does (in square distance space). Useful for comparing the original etable evaluation with the analytic evaluation.

References analytic_etable_evaluation(), bins_per_A2_, and core::conformation::Atom::xyz().

virtual Real core::scoring::etable::Etable::lj_radius ( int const  i) const
inlinevirtual
Real core::scoring::etable::Etable::lj_slope_intercept ( ) const
inline

References lj_slope_intercept_.

Real core::scoring::etable::Etable::lj_switch_dis2sigma ( ) const
inline

References lj_switch_dis2sigma_.

bool core::scoring::etable::Etable::lj_use_hbond_radii ( ) const
inline
bool core::scoring::etable::Etable::lj_use_lj_deriv_slope ( ) const
inline
bool core::scoring::etable::Etable::lj_use_water_radii ( ) const
inline
Real core::scoring::etable::Etable::lj_water_dis ( ) const
inline
Real core::scoring::etable::Etable::lj_water_hdis ( ) const
inline
Real core::scoring::etable::Etable::lj_wdepth ( int const  i) const
inline

Return the Lennard-Jones well depth for an atom.

References lj_wdepth_.

Referenced by precalc_etable_coefficients().

ObjexxFCL::FArray3D< Real > const& core::scoring::etable::Etable::ljatr ( ) const
inline
ObjexxFCL::FArray3D< Real > const& core::scoring::etable::Etable::ljrep ( ) const
inline
virtual Real core::scoring::etable::Etable::lk_dgfree ( int const  i) const
inlinevirtual

Return the Lazardis Karplus DGFree value for an atom.

Reimplemented in core::scoring::etable::MembEtable.

References lk_dgfree_.

Referenced by precalc_etable_coefficients().

Real core::scoring::etable::Etable::lk_inv_lambda2 ( int const  i) const
inline
virtual Real core::scoring::etable::Etable::lk_lambda ( int const  i) const
inlinevirtual

Return the Lazaridis Karplus "lambda" value (correlation distance) for an atom.

Reimplemented in core::scoring::etable::MembEtable.

References lk_lambda_.

Referenced by precalc_etable_coefficients().

Real core::scoring::etable::Etable::lk_min_dis2sigma ( ) const
inline
void core::scoring::etable::Etable::lk_solv_energy_and_deriv ( int  atype1,
int  atype2,
Real  dis,
Real solvE1,
Real solvE2,
Real dsolvE1,
Real dsolvE2 
) const
private

Analyticaly calculate the Lazaridis-Karplus solvation energy and derivatives for a pair of atoms at a given distance.

References lj_radius(), lk_coeff_, and lk_inv_lambda2_.

Referenced by calc_etable_value(), and smooth_etables_one_pair().

virtual Real core::scoring::etable::Etable::lk_volume ( int const  i) const
inlinevirtual

Return the Lazaridis Karplus volume for an atom.

Reimplemented in core::scoring::etable::MembEtable.

References lk_volume_.

Referenced by precalc_etable_coefficients().

Real core::scoring::etable::Etable::long_range_damping_length ( ) const
inline
void core::scoring::etable::Etable::make_pairenergy_table ( )
private

calculate fast lookup arrays for vdw and solvation energy

Several energies are precomputed when fullatom mode is initialized and stored in lookup tables to speed fullatom calculation. Currently pre-computed values are the Lennard-Jones van der Waals approximation (lj) and the Lazaridis-Karplus implicit solvation function (lk). For each of these energies the derivative w.r.t. atom pair separation distance is calculated and stored as well. Note that the lj energy is artificially divided into atractive and repulsive components.

Global Read:

pdbstatistics_pack.h: several threshold distances energy.h: just about everything should be used in the tree of etable functions

Global Write:

the etable: ljatr,dljatr,ljrep,dljrep,solvE

Remarks
References:
Author
ctsa 10-2003

References add_long_range_damping_, analytic_params_for_pair(), assign_parameters_to_full_etables(), atom_type(), bins_per_A2_, calc_etable_value(), calculate_normal_disbins(), damp_long_range(), dljatr(), dljatr_, dljrep(), dljrep_, dsolv1_, dsolv_, etable_disbins_, fa_hatr_, input_etable(), core::scoring::etable::EtableParamsOnePair::lj_r12_coeff, lj_r12_coeff_, core::scoring::etable::EtableParamsOnePair::lj_r6_coeff, lj_r6_coeff_, lj_sigma_, lj_switch_dis2sigma_, core::scoring::etable::EtableParamsOnePair::lj_switch_intercept, lj_switch_intercept_, lj_switch_sigma2dis_, core::scoring::etable::EtableParamsOnePair::lj_switch_slope, lj_switch_slope_, lj_switch_slope_sigma2wdepth_, lj_switch_value2wdepth_, ljatr(), ljatr_, ljrep(), ljrep_, core::scoring::etable::EtableParamsOnePair::ljrep_linear_ramp_d2_cutoff, core::scoring::etable::EtableParamsOnePair::lk_coeff1, core::scoring::etable::EtableParamsOnePair::lk_coeff2, lk_coeff_, lk_inv_lambda2_, core::scoring::etable::EtableParamsOnePair::lk_min_dis2sigma_value, lk_min_dis2sigma_value_, core::scoring::etable::EtableParamsOnePair::maxd2, modify_pot_one_pair(), n_atomtypes_, core::conformation::membrane::out, output_etable(), precalc_etable_coefficients(), safe_max_dis2_, slim_, smooth_etables_one_pair(), solv1_, solv2_, core::scoring::etable::TR(), and zero_hydrogen_and_water_ljatr_one_pair().

Referenced by Etable().

Real core::scoring::etable::Etable::max_dis ( ) const
inline
Real core::scoring::etable::Etable::max_dis2 ( ) const
inline
Real core::scoring::etable::Etable::max_heavy_heavy_cutoff ( ) const
inline

References max_dis_.

Real core::scoring::etable::Etable::max_heavy_hydrogen_cutoff ( ) const
inline
Real core::scoring::etable::Etable::max_hydrogen_hydrogen_cutoff ( ) const
inline
Real core::scoring::etable::Etable::max_hydrogen_lj_radius ( ) const

Returns the maximum lj radius for any hydrogen atom as defined by the input atom-type-set used to create this Etable.

References max_hydrogen_lj_radius_.

Real core::scoring::etable::Etable::max_non_hydrogen_lj_radius ( ) const

Returns the maximum lj radius for any non-hydrogen atom as defined by the atom-type-set used to create this Etable.

References max_non_hydrogen_lj_radius_.

Real core::scoring::etable::Etable::min_dis ( ) const
inline

References min_dis_.

Real core::scoring::etable::Etable::min_dis2 ( ) const
inline
void core::scoring::etable::Etable::modify_pot_one_pair ( Size  atype1,
Size  atype2,
ObjexxFCL::FArray1A< Real ljatr,
ObjexxFCL::FArray1A< Real dljatr,
ObjexxFCL::FArray1A< Real ljrep,
ObjexxFCL::FArray1A< Real dljrep,
ObjexxFCL::FArray1A< Real fasol1,
ObjexxFCL::FArray1A< Real fasol2,
ObjexxFCL::FArray1A< Real dfasol,
ObjexxFCL::FArray1A< Real dfasol1 
)
private

modify Etable to better treat 0-0, C-C, and H-H interactions

$$$ the Etables are modified in three ways: $$$ (1) the LK solvation energy is set to a constant below 4.2A to avoid shifting the position $$$ of the minimum on the LJatr potential. in refined decoys the peak in the C C pair $$$ distribution function shifts to around 3.8 A from ~4.0A in native structures; the LJatr $$$ potential has a minimum at 4.0A but this shifts towards smaller values because of the LK $$$ solvation term, which became increasingly favorable at shorter distances $$$ (2) the backbone carbonyl oxygen-carbonyl oxygen LJrep term has been modified to become $$$ moderately repulsive at distances less than 3.6A. this is to counteract the favorable $$$ LJatr between the atoms (which have radii of ~1.4A and so a minimum at ~2.8A; very few $$$ counts are observed in the pdb until around 3.2A) which leads to a significant shift in the $$$ O O pair distribution function towards smaller values in refined decoys. the repulsion is $$$ a temporary proxy for the lack of explicit electrostatic repulsion in the current force $$$ field. $$$ (3) a third soft repulsion between non polar hydrogens that was also based on comparison of $$$ refined decoy to native pdf's is currently commented out as the effects on packing have not $$$ been tested. it was observed that the protons tend to pile up at just beyond the point $$$ where the repulsion becomes strong, perhaps due to a general tendency to overcontraction $$$ because of long range LJatr interactions not compensated by interactions with solvent $$$ (which are of course missing)

Comments from DB: db the following function call modifies the potential in three ways: db (1) the solvation energy for nonpolar atoms is held constant below db 4.2A to avoid shifting the minimum in the LJ potential. db (2) a short range repulsion is added between backbone oxygens which are db otherwise brought too close together by the LJatr. db (3) the range of the repulsive interaction between non polar hydrogens is db increased slightly. (this is currently commented out because the effects db on design have not been tested)

Global Read:
pdbstatistics_pack.h: ljatr,dljatr,ljrep, dljrep, solv1,solv2,dsolv
Global Write:
pdbstatistics_pack.h: ljatr,dljatr,ljrep, dljrep, solv1,solv2,dsolv
Remarks
References:
Author
ctsa 10-2003

References analytic_params_for_pair(), atom_set(), atom_set_, bins_per_A2_, core::pack::dunbrack::c, carbon_types_, dljatr(), dljrep(), etable_disbins_, core::scoring::etable::ExtraQuadraticRepulsion::extrapolated_slope, core::scoring::etable::EtableParamsOnePair::fasol_final_weight, core::scoring::etable::EtableParamsOnePair::lj_minimum, ljatr(), core::scoring::etable::EtableParamsOnePair::ljatr_final_weight, ljrep(), core::scoring::etable::EtableParamsOnePair::ljrep_extra_repulsion, core::scoring::etable::EtableParamsOnePair::ljrep_from_negcrossing, protocols::mean_field::max(), core::scoring::etable::EtableParamsOnePair::maxd2, core::scoring::etable::ExtraQuadraticRepulsion::slope, core::scoring::etable::TR(), core::scoring::etable::ExtraQuadraticRepulsion::xhi, core::scoring::etable::ExtraQuadraticRepulsion::xlo, and core::scoring::etable::ExtraQuadraticRepulsion::ylo.

Referenced by make_pairenergy_table().

int core::scoring::etable::Etable::n_atomtypes ( ) const
inline
virtual Real core::scoring::etable::Etable::nblist_dis2_cutoff_HH ( ) const
inlinevirtual

The square distance cutoff beyond which any hydrogen/hydrogen pair is guaranteed to have an interaction energy of zero. This function is used by the NeighborList.

References nblist_dis2_cutoff_HH_.

virtual Real core::scoring::etable::Etable::nblist_dis2_cutoff_XH ( ) const
inlinevirtual

The square distance cutoff beyond which a hydrogen/heavy-atom pair is guaranteed to have an interaction energy of zero. This function is used by the NeighborList.

References nblist_dis2_cutoff_XH_.

virtual Real core::scoring::etable::Etable::nblist_dis2_cutoff_XX ( ) const
inlinevirtual

The square distance cutoff beyond which any pair of heavy-atoms is guaranteed to have an interaction energy of zero. This function is used by the NeighborList.

References nblist_dis2_cutoff_XX_.

void core::scoring::etable::Etable::output_etable ( ObjexxFCL::FArray3D< Real > &  etable,
std::string  label,
std::ostream &  out 
)
virtual

output an etable data file in the same format used in input_etable

$$$ file first line is <etable> <etable_disbins_> $$$ other lines are <atom type 1> <atomtype 1> <eval bin 1> <eval bin 2>...

Global Read:
pdbstatistics_pack.h: ljatr, dljatr, ljrep, dljrep, solv1,solv2,dsolv
Remarks
References:
Author
sheffler mar 19 2006

Reimplemented in core::scoring::etable::MembEtable.

References etable_disbins_, and n_atomtypes_.

Referenced by make_pairenergy_table().

void core::scoring::etable::Etable::precalc_etable_coefficients ( ObjexxFCL::FArray2< Real > &  lj_sigma,
ObjexxFCL::FArray2< Real > &  lj_r6_coeff,
ObjexxFCL::FArray2< Real > &  lj_r12_coeff,
ObjexxFCL::FArray2< Real > &  lj_switch_intercept,
ObjexxFCL::FArray2< Real > &  lj_switch_slope,
ObjexxFCL::FArray1< Real > &  lk_inv_lambda2,
ObjexxFCL::FArray2< Real > &  lk_coeff,
ObjexxFCL::FArray2< Real > &  lk_min_dis2sigma_value 
)
private

precalculate non-distance dependent coefficients of energy functions

Parameters
[out]lj_sigma- out - for atomtypes i and j: (radius_i+radius_j)
[out]lj_r6_coeff- out - precalced coefficient on the (1/dis)**6 term in lj
[out]lj_r12_coeff- out - precalced coefficient on the (1/dis)**12 term in lj
[out]lj_switch_intercept- out - for close contacts calculate lj from a line with this intercept
[out]lj_switch_slope- out - for close contacts calculate lj from a line with this slope
[out]lk_inv_lambda2- out - surprise! it's the 1/(lambda)**2 term in the lk equation
[out]lk_coeff- out - precalculation of all non-distance dependent terms outside of the exponential in the lk equation
[out]lk_min_dis2sigma_value- out - below the min dis2sigma ratio for lk, this value is assigned to the solvation
Global Read:
Global Write:
Remarks
References:
Author
ctsa 10-2003

References atom_type(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::chemical::AtomType::is_h2o(), core::chemical::AtomType::is_polar_hydrogen(), lj_hbond_dis_, lj_hbond_hdis_, lj_hbond_OH_donor_dis_, lj_radius(), lj_slope_intercept_, lj_switch_dis2sigma_, lj_switch_sigma2dis_, lj_switch_slope_sigma2wdepth_, lj_switch_value2wdepth_, lj_use_hbond_radii_, lj_use_lj_deriv_slope_, lj_use_water_radii_, lj_water_dis_, lj_water_hdis_, lj_wdepth(), lk_dgfree(), lk_inv_lambda2(), lk_lambda(), lk_min_dis2sigma_, lk_volume(), n_atomtypes_, core::chemical::AtomType::name(), and Wradius_.

Referenced by make_pairenergy_table().

void core::scoring::etable::Etable::read_alternate_parameter_set ( chemical::AtomTypeSetCAP  atom_set_in,
std::string const &  alternate_parameter_set 
)
private
void core::scoring::etable::Etable::smooth_etables_one_pair ( Size  atype1,
Size  atype2,
ObjexxFCL::FArray1A< Real ljatr,
ObjexxFCL::FArray1A< Real dljatr,
ObjexxFCL::FArray1A< Real ljrep,
ObjexxFCL::FArray1A< Real dljrep,
ObjexxFCL::FArray1A< Real fasol1,
ObjexxFCL::FArray1A< Real fasol2,
ObjexxFCL::FArray1A< Real dfasol,
ObjexxFCL::FArray1A< Real dfasol1 
)
private
virtual ObjexxFCL::FArray3D< Real > const& core::scoring::etable::Etable::solv1 ( ) const
inlinevirtual

Reimplemented in core::scoring::etable::MembEtable.

References solv1_.

virtual ObjexxFCL::FArray3D< Real > const& core::scoring::etable::Etable::solv2 ( ) const
inlinevirtual

Reimplemented in core::scoring::etable::MembEtable.

References solv2_.

Real core::scoring::etable::Etable::Wradius ( ) const
inline
void core::scoring::etable::Etable::zero_hydrogen_and_water_ljatr_one_pair ( Size  atype1,
Size  atype2,
ObjexxFCL::FArray1A< Real ljrep,
ObjexxFCL::FArray1A< Real ljatr,
ObjexxFCL::FArray1A< Real dljatr,
ObjexxFCL::FArray1A< Real fasol1,
ObjexxFCL::FArray1A< Real fasol2,
ObjexxFCL::FArray1A< Real dfasol,
ObjexxFCL::FArray1A< Real dfasol1 
)
private

Member Data Documentation

bool const core::scoring::etable::Etable::add_long_range_damping_
private
utility::vector1< EtableParamsOnePair > core::scoring::etable::Etable::analytic_parameters_
private
chemical::AtomTypeSetCAP core::scoring::etable::Etable::atom_set_
private
int const core::scoring::etable::Etable::bins_per_A2_
private
utility::vector1< Size > core::scoring::etable::Etable::carbon_types_
private
ObjexxFCL::FArray3D< Real > core::scoring::etable::Etable::dljatr_
private
ObjexxFCL::FArray3D< Real > core::scoring::etable::Etable::dljrep_
private
ObjexxFCL::FArray3D< Real > core::scoring::etable::Etable::dsolv1_
private
ObjexxFCL::FArray3D< Real > core::scoring::etable::Etable::dsolv_
private
bool const core::scoring::etable::Etable::enlarge_h_lj_wdepth_
private
Real const core::scoring::etable::Etable::epsilon_
private
int const core::scoring::etable::Etable::etable_disbins_
private
bool core::scoring::etable::Etable::fa_hatr_
private
Real core::scoring::etable::Etable::fasol_cubic_poly_far_xhi_
private
Real core::scoring::etable::Etable::fasol_cubic_poly_far_xlo_
private

Data needed to describe the splines for the fasol term: There are two cubic_polys needed: one to smooth the transition to where the fasol term goes flat as the distance becomes less than the sum of the van der Waals radii (the "close" cubic_poly), and a second to smooth the transition where the distance goes to the fa_max_dis and the energy goes to 0 (the far cubic_poly). In between the close and far values, the exponential form of the energy function is used.

Referenced by analytic_etable_derivatives(), analytic_lk_derivatives(), analytic_lk_evaluation(), analytic_lk_evaluation_individual(), fasol_cubic_poly_far_xlo(), and smooth_etables_one_pair().

Real core::scoring::etable::Etable::hydrogen_interaction_cutoff2_
private
Real const core::scoring::etable::Etable::lj_hbond_dis_
private
Real const core::scoring::etable::Etable::lj_hbond_hdis_
private
Real const core::scoring::etable::Etable::lj_hbond_OH_donor_dis_
private
ObjexxFCL::FArray2D< Real > core::scoring::etable::Etable::lj_r12_coeff_
private
ObjexxFCL::FArray2D< Real > core::scoring::etable::Etable::lj_r6_coeff_
private
utility::vector1< Real > core::scoring::etable::Etable::lj_radius_
private
ObjexxFCL::FArray2D< Real > core::scoring::etable::Etable::lj_sigma_
private
Real const core::scoring::etable::Etable::lj_slope_intercept_
private
Real const core::scoring::etable::Etable::lj_switch_dis2sigma_
private
ObjexxFCL::FArray2D< Real > core::scoring::etable::Etable::lj_switch_intercept_
private
Real core::scoring::etable::Etable::lj_switch_sigma2dis_
private
ObjexxFCL::FArray2D< Real > core::scoring::etable::Etable::lj_switch_slope_
private
Real core::scoring::etable::Etable::lj_switch_slope_sigma2wdepth_
private
Real core::scoring::etable::Etable::lj_switch_value2wdepth_
private
bool const core::scoring::etable::Etable::lj_use_hbond_radii_
private
bool const core::scoring::etable::Etable::lj_use_lj_deriv_slope_
private
bool const core::scoring::etable::Etable::lj_use_water_radii_
private
Real const core::scoring::etable::Etable::lj_water_dis_
private
Real const core::scoring::etable::Etable::lj_water_hdis_
private
utility::vector1< Real > core::scoring::etable::Etable::lj_wdepth_
private
ObjexxFCL::FArray3D< Real > core::scoring::etable::Etable::ljatr_
private
ObjexxFCL::FArray3D< Real > core::scoring::etable::Etable::ljrep_
private
ObjexxFCL::FArray2D< Real > core::scoring::etable::Etable::lk_coeff_
private
utility::vector1< Real > core::scoring::etable::Etable::lk_dgfree_
private
ObjexxFCL::FArray1D< Real > core::scoring::etable::Etable::lk_inv_lambda2_
private
utility::vector1< Real > core::scoring::etable::Etable::lk_lambda_
private
Real const core::scoring::etable::Etable::lk_min_dis2sigma_
private
ObjexxFCL::FArray2D< Real > core::scoring::etable::Etable::lk_min_dis2sigma_value_
private
utility::vector1< Real > core::scoring::etable::Etable::lk_volume_
private
Real const core::scoring::etable::Etable::long_range_damping_length_
private
Real const core::scoring::etable::Etable::max_dis2_
private
Real const core::scoring::etable::Etable::max_dis_
private
Real core::scoring::etable::Etable::max_heavy_hydrogen_cutoff_
private
Real core::scoring::etable::Etable::max_hydrogen_hydrogen_cutoff_
private
Real core::scoring::etable::Etable::max_hydrogen_lj_radius_
private
Real core::scoring::etable::Etable::max_non_hydrogen_lj_radius_
private
Real const core::scoring::etable::Etable::min_dis2_
private
Real const core::scoring::etable::Etable::min_dis_
private

Referenced by min_dis().

int const core::scoring::etable::Etable::n_atomtypes_
private
Real core::scoring::etable::Etable::nblist_dis2_cutoff_HH_
private
Real core::scoring::etable::Etable::nblist_dis2_cutoff_XH_
private
Real core::scoring::etable::Etable::nblist_dis2_cutoff_XX_
private
bool const core::scoring::etable::Etable::no_lk_polar_desolvation_
private
bool const core::scoring::etable::Etable::proline_N_is_lk_nonpolar_
private
Real const core::scoring::etable::Etable::safe_max_dis2_
private
bool core::scoring::etable::Etable::slim_
private
ObjexxFCL::FArray3D< Real > core::scoring::etable::Etable::solv1_
private
ObjexxFCL::FArray3D< Real > core::scoring::etable::Etable::solv2_
private
Real const core::scoring::etable::Etable::Wradius_
private

The documentation for this class was generated from the following files: