Class definition for Etable. More...

#include <Etable.hh>

Inheritance diagram for core::scoring::etable::Etable:

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...

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< Real >	lj_sigma_

ObjexxFCL::FArray2D< Real >	lj_r6_coeff_

ObjexxFCL::FArray2D< Real >	lj_r12_coeff_

ObjexxFCL::FArray2D< Real >	lj_switch_intercept_

ObjexxFCL::FArray2D< Real >	lj_switch_slope_

ObjexxFCL::FArray1D< Real >	lk_inv_lambda2_

ObjexxFCL::FArray2D< Real >	lk_coeff_

ObjexxFCL::FArray2D< Real >	lk_min_dis2sigma_value_

Real	fasol_cubic_poly_far_xlo_

Real	fasol_cubic_poly_far_xhi_

utility::vector1< Real >	lj_radius_

utility::vector1< Real >	lj_wdepth_

utility::vector1< Real >	lk_dgfree_

utility::vector1< Real >	lk_volume_

utility::vector1< Real >	lk_lambda_

ObjexxFCL::FArray3D< Real >	ljatr_

ObjexxFCL::FArray3D< Real >	ljrep_

ObjexxFCL::FArray3D< Real >	solv1_

ObjexxFCL::FArray3D< Real >	solv2_

ObjexxFCL::FArray3D< Real >	dljatr_

ObjexxFCL::FArray3D< Real >	dljrep_

ObjexxFCL::FArray3D< Real >	dsolv_

ObjexxFCL::FArray3D< Real >	dsolv1_

utility::vector1< Size >	carbon_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

References add_long_range_damping_.

Referenced by core::scoring::etable::MembEtable::make_pairenergy_table().

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

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().

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

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().

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

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().

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

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().

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

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.

Referenced by analytic_etable_evaluation().

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

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.

Referenced by analytic_lk_energy().

EtableParamsOnePair const & core::scoring::etable::Etable::analytic_params_for_pair	(	Size	atype1,
		Size	atype2
	)		const

inline

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().

EtableParamsOnePair & core::scoring::etable::Etable::analytic_params_for_pair	(	Size	atype1,
		Size	atype2
	)

inlineprivate

References analytic_parameters_, and n_atomtypes_.

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

References dljatr(), dljatr_, dljrep(), dljrep_, dsolv1_, dsolv_, etable_disbins_, ljatr(), ljatr_, ljrep(), ljrep_, solv1_, and solv2_.

Referenced by make_pairenergy_table().

chemical::AtomTypeSetCAP core::scoring::etable::Etable::atom_set ( ) const

inline

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().

chemical::AtomType const& core::scoring::etable::Etable::atom_type ( int const type )

inline

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().

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

References fa_hatr_, hydrogen_interaction_cutoff2_, protocols::mean_field::max(), core::chemical::MAX_CHEMICAL_BOND_TO_HYDROGEN_LENGTH, max_dis_, max_hydrogen_lj_radius_, and max_non_hydrogen_lj_radius_.

Referenced by Etable().

void core::scoring::etable::Etable::calculate_nblist_distance_thresholds ( EtableOptions const & options )

private

References fa_hatr_, core::scoring::etable::EtableOptions::max_dis, max_dis_, max_heavy_hydrogen_cutoff_, max_hydrogen_hydrogen_cutoff_, max_hydrogen_lj_radius_, max_non_hydrogen_lj_radius_, nblist_dis2_cutoff_HH_, nblist_dis2_cutoff_XH_, and nblist_dis2_cutoff_XX_.

Referenced by Etable().

int core::scoring::etable::Etable::calculate_normal_disbins ( ) const

private

References add_long_range_damping_, bins_per_A2_, etable_disbins_, long_range_damping_length_, max_dis2_, and max_dis_.

Referenced by make_pairenergy_table().

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

References bins_per_A2_, dljatr(), dljrep(), etable_disbins_, ljatr(), ljrep(), long_range_damping_length_, and max_dis_.

Referenced by make_pairenergy_table().

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

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().

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

inline

References dljrep_.

Referenced by assign_parameters_to_full_etables(), damp_long_range(), make_pairenergy_table(), modify_pot_one_pair(), and smooth_etables_one_pair().

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

References epsilon_.

Referenced by core::scoring::etable::MembEtable::calc_etable_value().

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

inline

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().

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

References fasol_cubic_poly_far_xhi_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_eval_etable_split_fasol().

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

inline

References fasol_cubic_poly_far_xlo_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_eval_etable_split_fasol().

int core::scoring::etable::Etable::get_bins_per_A2 ( ) const

inline

References bins_per_A2_.

Referenced by core::scoring::etable::MembEtable::make_pairenergy_table(), and core::scoring::etable::MembEtable::smooth_etables().

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

inline

References lj_hbond_dis_.

Referenced by core::scoring::etable::MembEtable::precalc_etable_coefficients().

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

inline

References lj_hbond_hdis_.

Referenced by core::scoring::etable::MembEtable::precalc_etable_coefficients().

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

inline

References lj_hbond_OH_donor_dis_.

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

References hydrogen_interaction_cutoff2_.

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

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().

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

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().

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

References lj_use_hbond_radii_.

Referenced by core::scoring::etable::MembEtable::precalc_etable_coefficients().

bool core::scoring::etable::Etable::lj_use_lj_deriv_slope ( ) const

inline

References lj_use_lj_deriv_slope_.

bool core::scoring::etable::Etable::lj_use_water_radii ( ) const

inline

References lj_use_water_radii_.

Referenced by core::scoring::etable::MembEtable::precalc_etable_coefficients().

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

inline

References lj_water_dis_.

Referenced by core::scoring::etable::MembEtable::precalc_etable_coefficients().

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

inline

References lj_water_hdis_.

Referenced by core::scoring::etable::MembEtable::precalc_etable_coefficients().

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

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().

ObjexxFCL::FArray3D< Real > const& core::scoring::etable::Etable::ljrep ( ) const

inline

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().

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

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().

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

References lk_min_dis2sigma_.

Referenced by core::scoring::etable::MembEtable::calc_etable_value(), and core::scoring::etable::MembEtable::precalc_etable_coefficients().

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

References long_range_damping_length_.

Referenced by core::scoring::etable::MembEtable::make_pairenergy_table().

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

Referenced by Etable().

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

inline

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().

Real core::scoring::etable::Etable::max_dis2 ( ) const

inline

References max_dis2_.

Referenced by core::scoring::etable::MembEtable::calc_etable_value(), protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_eval_etable_split_fasol(), and core::scoring::etable::MembEtable::make_pairenergy_table().

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

References max_heavy_hydrogen_cutoff_.

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

inline

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_.

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

inline

References min_dis_.

Real core::scoring::etable::Etable::min_dis2 ( ) const

inline

References min_dis2_.

Referenced by core::scoring::etable::MembEtable::calc_etable_value(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_eval_etable_split_fasol().

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

Referenced by make_pairenergy_table().

int core::scoring::etable::Etable::n_atomtypes ( ) const

inline

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().

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

References lj_radius_, lj_wdepth_, lk_dgfree_, lk_lambda_, lk_volume_, n_atomtypes_, and core::scoring::etable::TR().

Referenced by Etable().

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

Referenced by make_pairenergy_table().

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

References Wradius_.

Referenced by core::scoring::etable::MembEtable::precalc_etable_coefficients().

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

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().

Member Data Documentation

bool const core::scoring::etable::Etable::add_long_range_damping_

private

Referenced by add_long_range_damping(), calculate_normal_disbins(), and make_pairenergy_table().

utility::vector1< EtableParamsOnePair > core::scoring::etable::Etable::analytic_parameters_

private

Referenced by analytic_params_for_pair(), and dimension_etable_arrays().

chemical::AtomTypeSetCAP core::scoring::etable::Etable::atom_set_

private

Referenced by atom_set(), atom_type(), initialize_carbontypes_to_linearize_fasol(), initialize_from_input_atomset(), modify_pot_one_pair(), and zero_hydrogen_and_water_ljatr_one_pair().

int const core::scoring::etable::Etable::bins_per_A2_

private

Referenced by calculate_normal_disbins(), damp_long_range(), get_bins_per_A2(), interpolated_analytic_etable_evaluation(), make_pairenergy_table(), modify_pot_one_pair(), and smooth_etables_one_pair().

utility::vector1< Size > core::scoring::etable::Etable::carbon_types_

private

Referenced by initialize_carbontypes_to_linearize_fasol(), and modify_pot_one_pair().

ObjexxFCL::FArray3D< Real > core::scoring::etable::Etable::dljatr_

private

Referenced by assign_parameters_to_full_etables(), dimension_etable_arrays(), dljatr(), and make_pairenergy_table().

ObjexxFCL::FArray3D< Real > core::scoring::etable::Etable::dljrep_

private

Referenced by assign_parameters_to_full_etables(), dimension_etable_arrays(), dljrep(), and make_pairenergy_table().

ObjexxFCL::FArray3D< Real > core::scoring::etable::Etable::dsolv1_

private

Referenced by assign_parameters_to_full_etables(), dimension_etable_arrays(), dsolv1(), and make_pairenergy_table().

ObjexxFCL::FArray3D< Real > core::scoring::etable::Etable::dsolv_

private

Referenced by assign_parameters_to_full_etables(), dimension_etable_arrays(), dsolv(), and make_pairenergy_table().

bool const core::scoring::etable::Etable::enlarge_h_lj_wdepth_

private

Referenced by initialize_from_input_atomset().

Real const core::scoring::etable::Etable::epsilon_

private

Referenced by analytic_etable_derivatives(), analytic_etable_evaluation(), analytic_lk_derivatives(), analytic_lk_energy(), calc_etable_value(), and epsilon().

int const core::scoring::etable::Etable::etable_disbins_

private

Referenced by assign_parameters_to_full_etables(), calculate_normal_disbins(), damp_long_range(), dimension_etable_arrays(), etable_disbins(), input_etable(), make_pairenergy_table(), modify_pot_one_pair(), output_etable(), smooth_etables_one_pair(), and zero_hydrogen_and_water_ljatr_one_pair().

bool core::scoring::etable::Etable::fa_hatr_

private

Referenced by calculate_hydrogen_atom_reach(), calculate_nblist_distance_thresholds(), fa_hatr(), and make_pairenergy_table().

Real core::scoring::etable::Etable::fasol_cubic_poly_far_xhi_

private

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

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().