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Rosetta
2020.50
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Class definition for Etable. More...
#include <Etable.hh>
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... | |
EtableParamsOnePair & | analytic_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... | |
Class definition for Etable.
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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 = "" |
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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().
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References add_long_range_damping_.
Referenced by core::scoring::etable::MembEtable::make_pairenergy_table().
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Analytically evaluate the energy derivatives for a pair of atoms.
References analytic_ljatr_cubic_poly_ramp_to_zero_deriv(), analytic_params_for_pair(), epsilon_, core::scoring::etable::ExtraQuadraticRepulsion::extrapolated_slope, 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 protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), and core::scoring::etable::AnalyticEtableEvaluator::eval_dE_dR_over_r().
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Use an analytic functional form of the etable to evaluate an atom-pair energy without reading from the enormous and uncachable tables.
References analytic_lj_generic_form(), analytic_ljatr_cubic_poly_ramp_to_zero(), analytic_ljrep_linearized(), analytic_lk_evaluation(), analytic_params_for_pair(), epsilon_, core::scoring::etable::ExtraQuadraticRepulsion::extrapolated_slope, max_dis2_, min_dis2_, core::conformation::Atom::type(), and core::conformation::Atom::xyz().
Referenced by core::scoring::etable::AnalyticEtableEvaluator::atom_pair_energy(), and interpolated_analytic_etable_evaluation().
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: 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().
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: 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().
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: 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().
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only to be called when the distance, dis, is less than the switch-point for the lj_switch_dis2sigma value.
References core::scoring::etable::EtableParamsOnePair::lj_switch_intercept, core::scoring::etable::EtableParamsOnePair::lj_switch_slope, and core::scoring::etable::EtableParamsOnePair::ljrep_linear_ramp_d2_cutoff.
Referenced by analytic_etable_evaluation().
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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().
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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.
References analytic_lk_evaluation_individual(), analytic_params_for_pair(), epsilon_, 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(), core::scoring::etable::AnalyticEtableEvaluator::atom_pair_lk_energy_and_deriv_v_efficient(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), and core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges().
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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.
Note that atype1 must be less than or equal to atype2; the EtableParamsOnePair are stored only once for atom types i and j.
References core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly_close, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly_close_end, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly_close_flat, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly_close_start, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly_far, fasol_cubic_poly_far_xhi_, fasol_cubic_poly_far_xlo_, core::scoring::etable::EtableParamsOnePair::fasol_final_weight, lj_radius(), core::scoring::etable::EtableParamsOnePair::lk_coeff1, core::scoring::etable::EtableParamsOnePair::lk_coeff2, and lk_inv_lambda2_.
Referenced by analytic_etable_evaluation().
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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.
The etable parameters are stored such that the atom type of atom 1 is less than or equal to the atom type of atom 2, so that the caller of this function will need to keep track of which atom is which.
References core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly1_close, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly1_close_flat, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly1_far, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly2_close, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly2_close_flat, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly2_far, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly_close_end, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly_close_start, fasol_cubic_poly_far_xhi_, fasol_cubic_poly_far_xlo_, core::scoring::etable::EtableParamsOnePair::fasol_final_weight, lj_radius(), core::scoring::etable::EtableParamsOnePair::lk_coeff1, core::scoring::etable::EtableParamsOnePair::lk_coeff2, and lk_inv_lambda2_.
Referenced by analytic_lk_energy().
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References analytic_parameters_, and n_atomtypes_.
Referenced by analytic_etable_derivatives(), analytic_etable_evaluation(), analytic_lk_derivatives(), analytic_lk_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_eval_etable_split_fasol(), make_pairenergy_table(), modify_pot_one_pair(), smooth_etables_one_pair(), and zero_hydrogen_and_water_ljatr_one_pair().
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References analytic_parameters_, and n_atomtypes_.
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References atom_set_.
Referenced by atom_type(), initialize_carbontypes_to_linearize_fasol(), initialize_from_input_atomset(), core::scoring::etable::MembEtable::modify_pot(), modify_pot_one_pair(), core::scoring::etable::TableLookupEtableEnergy::setup_for_scoring_(), core::scoring::etable::AnalyticEtableEnergy::setup_for_scoring_(), and zero_hydrogen_and_water_ljatr_one_pair().
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References atom_set(), and atom_set_.
Referenced by make_pairenergy_table(), core::scoring::etable::MembEtable::precalc_etable_coefficients(), precalc_etable_coefficients(), and zero_hydrogen_and_water_ljatr_one_pair().
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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
[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 |
pdbstatistics_pack.h etable.h
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().
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References add_long_range_damping_, bins_per_A2_, etable_disbins_, long_range_damping_length_, max_dis2_, and max_dis_.
Referenced by make_pairenergy_table().
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References bins_per_A2_, dljatr(), dljrep(), etable_disbins_, ljatr(), ljrep(), long_range_damping_length_, and max_dis_.
Referenced by make_pairenergy_table().
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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().
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const access to the deriv arrays
References dljatr_.
Referenced by assign_parameters_to_full_etables(), damp_long_range(), make_pairenergy_table(), modify_pot_one_pair(), smooth_etables_one_pair(), and zero_hydrogen_and_water_ljatr_one_pair().
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References dljrep_.
Referenced by assign_parameters_to_full_etables(), damp_long_range(), make_pairenergy_table(), modify_pot_one_pair(), and smooth_etables_one_pair().
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return the solvation derivative table that combines atom1 and atom2's desolvations
References dsolv_.
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return the solvation derivative table for the desolvation of atom1 by atom2
Reimplemented in core::scoring::etable::MembEtable.
References dsolv1_.
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References epsilon_.
Referenced by core::scoring::etable::MembEtable::calc_etable_value().
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References etable_disbins_.
Referenced by core::scoring::etable::MembEtable::dimension_memb_etable_arrays(), core::scoring::etable::MembEtable::input_etable(), core::scoring::etable::MembEtable::make_pairenergy_table(), core::scoring::etable::MembEtable::modify_pot(), core::scoring::etable::MembEtable::output_etable(), and core::scoring::etable::MembEtable::smooth_etables().
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Do hydrogens provide attractive forces or do they only repell?
References fa_hatr_.
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References fasol_cubic_poly_far_xhi_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_eval_etable_split_fasol().
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References fasol_cubic_poly_far_xlo_.
Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_eval_etable_split_fasol().
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References bins_per_A2_.
Referenced by core::scoring::etable::MembEtable::make_pairenergy_table(), and core::scoring::etable::MembEtable::smooth_etables().
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References lj_hbond_dis_.
Referenced by core::scoring::etable::MembEtable::precalc_etable_coefficients().
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References lj_hbond_hdis_.
Referenced by core::scoring::etable::MembEtable::precalc_etable_coefficients().
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References lj_hbond_OH_donor_dis_.
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References safe_max_dis2_.
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References hydrogen_interaction_cutoff2_.
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References atom_set(), atom_set_, and carbon_types_.
Referenced by Etable().
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References atom_set(), atom_set_, core::chemical::enlarge_h_lj_wdepth(), enlarge_h_lj_wdepth_, lj_radius_, lj_wdepth_, lk_dgfree_, lk_lambda_, lk_volume_, max_hydrogen_lj_radius_, max_non_hydrogen_lj_radius_, n_atomtypes_, no_lk_polar_desolvation_, and proline_N_is_lk_nonpolar_.
Referenced by Etable().
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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>...
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().
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Return the Lennard-Jones radius for an atom.
Reimplemented in core::scoring::etable::MembEtable.
References lj_radius_.
Referenced by analytic_etable_derivatives(), analytic_lk_derivatives(), analytic_lk_evaluation(), analytic_lk_evaluation_individual(), protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_eval_etable_split_fasol(), lk_solv_energy_and_deriv(), and precalc_etable_coefficients().
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References lj_slope_intercept_.
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References lj_switch_dis2sigma_.
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References lj_use_hbond_radii_.
Referenced by core::scoring::etable::MembEtable::precalc_etable_coefficients().
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References lj_use_lj_deriv_slope_.
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References lj_use_water_radii_.
Referenced by core::scoring::etable::MembEtable::precalc_etable_coefficients().
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References lj_water_dis_.
Referenced by core::scoring::etable::MembEtable::precalc_etable_coefficients().
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References lj_water_hdis_.
Referenced by core::scoring::etable::MembEtable::precalc_etable_coefficients().
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Return the Lennard-Jones well depth for an atom.
References lj_wdepth_.
Referenced by precalc_etable_coefficients().
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const access to the arrays
References ljatr_.
Referenced by assign_parameters_to_full_etables(), damp_long_range(), make_pairenergy_table(), modify_pot_one_pair(), smooth_etables_one_pair(), and zero_hydrogen_and_water_ljatr_one_pair().
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References ljrep_.
Referenced by assign_parameters_to_full_etables(), damp_long_range(), make_pairenergy_table(), modify_pot_one_pair(), smooth_etables_one_pair(), and zero_hydrogen_and_water_ljatr_one_pair().
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Return the Lazardis Karplus DGFree value for an atom.
Reimplemented in core::scoring::etable::MembEtable.
References lk_dgfree_.
Referenced by precalc_etable_coefficients().
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References lk_inv_lambda2_.
Referenced by core::scoring::etable::MembEtable::calc_etable_value(), protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_eval_etable_split_fasol(), core::scoring::etable::MembEtable::make_pairenergy_table(), core::scoring::etable::MembEtable::precalc_etable_coefficients(), and precalc_etable_coefficients().
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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().
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References lk_min_dis2sigma_.
Referenced by core::scoring::etable::MembEtable::calc_etable_value(), and core::scoring::etable::MembEtable::precalc_etable_coefficients().
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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().
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Return the Lazaridis Karplus volume for an atom.
Reimplemented in core::scoring::etable::MembEtable.
References lk_volume_.
Referenced by precalc_etable_coefficients().
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References long_range_damping_length_.
Referenced by core::scoring::etable::MembEtable::make_pairenergy_table().
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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.
pdbstatistics_pack.h: several threshold distances energy.h: just about everything should be used in the tree of etable functions
the etable: ljatr,dljatr,ljrep,dljrep,solvE
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().
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References max_dis_.
Referenced by core::energy_methods::Fa_MbsolvEnergy::atomic_interaction_cutoff(), core::energy_methods::RNA_LJ_BaseEnergy::atomic_interaction_cutoff(), core::energy_methods::LK_hack::atomic_interaction_cutoff(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::etable::MembEtable::make_pairenergy_table(), and core::scoring::etable::MembEtable::smooth_etables().
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References max_heavy_hydrogen_cutoff_.
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References max_hydrogen_hydrogen_cutoff_.
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_.
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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)
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().
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References n_atomtypes_.
Referenced by core::scoring::etable::MembEtable::dimension_memb_etable_arrays(), core::scoring::etable::MembEtable::initialize_from_atomset(), core::scoring::etable::MembEtable::make_pairenergy_table(), core::scoring::etable::MembEtable::output_etable(), core::scoring::etable::MembEtable::precalc_etable_coefficients(), and core::scoring::etable::MembEtable::smooth_etables().
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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_.
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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_.
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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_.
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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>...
Reimplemented in core::scoring::etable::MembEtable.
References etable_disbins_, and n_atomtypes_.
Referenced by make_pairenergy_table().
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precalculate non-distance dependent coefficients of energy functions
[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 |
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().
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References lj_radius_, lj_wdepth_, lk_dgfree_, lk_lambda_, lk_volume_, n_atomtypes_, and core::scoring::etable::TR().
Referenced by Etable().
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References analytic_params_for_pair(), bins_per_A2_, dljatr(), dljrep(), etable_disbins_, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly1_close, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly1_close_flat, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly1_far, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly2_close, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly2_close_flat, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly2_far, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly_close, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly_close_end, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly_close_flat, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly_close_start, core::scoring::etable::EtableParamsOnePair::fasol_cubic_poly_far, fasol_cubic_poly_far_xhi_, fasol_cubic_poly_far_xlo_, core::scoring::etable::EtableParamsOnePair::lj_minimum, lj_sigma_, core::scoring::etable::EtableParamsOnePair::lj_val_at_minimum, lj_wdepth_, ljatr(), core::scoring::etable::EtableParamsOnePair::ljatr_cubic_poly_parameters, core::scoring::etable::EtableParamsOnePair::ljatr_cubic_poly_xhi, core::scoring::etable::EtableParamsOnePair::ljatr_cubic_poly_xlo, ljrep(), lk_solv_energy_and_deriv(), protocols::mean_field::max(), max_dis_, protocols::mean_field::min(), protocols::loops::start, and core::scoring::etable::TR().
Referenced by make_pairenergy_table().
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Reimplemented in core::scoring::etable::MembEtable.
References solv1_.
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Reimplemented in core::scoring::etable::MembEtable.
References solv2_.
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References Wradius_.
Referenced by core::scoring::etable::MembEtable::precalc_etable_coefficients().
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References analytic_params_for_pair(), atom_set(), atom_set_, atom_type(), dljatr(), etable_disbins_, core::scoring::etable::EtableParamsOnePair::fasol_final_weight, core::scoring::etable::EtableParamsOnePair::hydrogen_interaction, lj_sigma_, ljatr(), core::scoring::etable::EtableParamsOnePair::ljatr_final_weight, ljrep(), and core::scoring::etable::EtableParamsOnePair::maxd2.
Referenced by make_pairenergy_table().
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Referenced by add_long_range_damping(), calculate_normal_disbins(), and make_pairenergy_table().
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Referenced by analytic_params_for_pair(), and dimension_etable_arrays().
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Referenced by initialize_carbontypes_to_linearize_fasol(), and modify_pot_one_pair().
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Referenced by assign_parameters_to_full_etables(), dimension_etable_arrays(), dljatr(), and make_pairenergy_table().
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Referenced by assign_parameters_to_full_etables(), dimension_etable_arrays(), dljrep(), and make_pairenergy_table().
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Referenced by assign_parameters_to_full_etables(), dimension_etable_arrays(), dsolv1(), and make_pairenergy_table().
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Referenced by assign_parameters_to_full_etables(), dimension_etable_arrays(), dsolv(), and make_pairenergy_table().
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Referenced by initialize_from_input_atomset().
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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().
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Referenced by calculate_hydrogen_atom_reach(), and hydrogen_interaction_cutoff2().
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Referenced by get_lj_hbond_dis(), and precalc_etable_coefficients().
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Referenced by get_lj_hbond_hdis(), and precalc_etable_coefficients().
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Referenced by get_lj_hbond_OH_donor_dis(), and precalc_etable_coefficients().
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Referenced by calc_etable_value(), dimension_etable_arrays(), and make_pairenergy_table().
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Referenced by calc_etable_value(), dimension_etable_arrays(), and make_pairenergy_table().
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Referenced by dimension_etable_arrays(), initialize_from_input_atomset(), lj_radius(), and read_alternate_parameter_set().
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Referenced by lj_slope_intercept(), and precalc_etable_coefficients().
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Referenced by calc_etable_value(), lj_switch_dis2sigma(), make_pairenergy_table(), and precalc_etable_coefficients().
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Referenced by calc_etable_value(), dimension_etable_arrays(), and make_pairenergy_table().
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Referenced by make_pairenergy_table(), and precalc_etable_coefficients().
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Referenced by calc_etable_value(), dimension_etable_arrays(), and make_pairenergy_table().
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Referenced by make_pairenergy_table(), and precalc_etable_coefficients().
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Referenced by make_pairenergy_table(), and precalc_etable_coefficients().
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Referenced by lj_use_hbond_radii(), and precalc_etable_coefficients().
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Referenced by lj_use_lj_deriv_slope(), and precalc_etable_coefficients().
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Referenced by lj_use_water_radii(), and precalc_etable_coefficients().
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Referenced by lj_water_dis(), and precalc_etable_coefficients().
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Referenced by lj_water_hdis(), and precalc_etable_coefficients().
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Referenced by assign_parameters_to_full_etables(), dimension_etable_arrays(), ljatr(), and make_pairenergy_table().
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Referenced by assign_parameters_to_full_etables(), dimension_etable_arrays(), ljrep(), and make_pairenergy_table().
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Referenced by dimension_etable_arrays(), lk_solv_energy_and_deriv(), and make_pairenergy_table().
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Referenced by dimension_etable_arrays(), initialize_from_input_atomset(), lk_dgfree(), and read_alternate_parameter_set().
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Referenced by dimension_etable_arrays(), initialize_from_input_atomset(), lk_lambda(), and read_alternate_parameter_set().
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Referenced by calc_etable_value(), lk_min_dis2sigma(), and precalc_etable_coefficients().
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Referenced by calc_etable_value(), dimension_etable_arrays(), and make_pairenergy_table().
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Referenced by dimension_etable_arrays(), initialize_from_input_atomset(), lk_volume(), and read_alternate_parameter_set().
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Referenced by calculate_normal_disbins(), damp_long_range(), and long_range_damping_length().
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Referenced by calculate_nblist_distance_thresholds(), and max_heavy_hydrogen_cutoff().
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Referenced by calculate_nblist_distance_thresholds(), and max_hydrogen_hydrogen_cutoff().
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Referenced by calculate_nblist_distance_thresholds(), and nblist_dis2_cutoff_HH().
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Referenced by calculate_nblist_distance_thresholds(), and nblist_dis2_cutoff_XH().
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Referenced by calculate_nblist_distance_thresholds(), and nblist_dis2_cutoff_XX().
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Referenced by initialize_from_input_atomset().
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Referenced by initialize_from_input_atomset().
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Referenced by get_safe_max_dis2(), and make_pairenergy_table().
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Referenced by dimension_etable_arrays(), and make_pairenergy_table().
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Referenced by assign_parameters_to_full_etables(), dimension_etable_arrays(), make_pairenergy_table(), and solv1().
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Referenced by assign_parameters_to_full_etables(), dimension_etable_arrays(), make_pairenergy_table(), and solv2().
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Referenced by precalc_etable_coefficients(), and Wradius().