jk Class definition for Etable More...

#include <Etable.hh>

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

Collaboration diagram for core::scoring::etable::Etable:

Public Member Functions
virtual	~Etable ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	Etable (chemical::AtomTypeSetCAP atom_set_in, EtableOptions const &options, std::string const alternate_parameter_set="")
	constructor More...

Size	n_atomtypes () const

ObjexxFCL::FArray3D< Real > const &	ljatr () const
	const access to the arrays More...

ObjexxFCL::FArray3D< Real > const &	ljrep () const

ObjexxFCL::FArray3D< Real > const &	solv1 () const

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

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	get_safe_max_dis2 () const

int	get_bins_per_A2 () const

chemical::AtomTypeSetCAP	atom_set () const

Real	hydrogen_interaction_cutoff2 () const

Real	max_heavy_heavy_cutoff () const

Real	max_heavy_hydrogen_cutoff () const

Real	max_hydrogen_hydrogen_cutoff () const

Real	nblist_dis2_cutoff_XX () const

Real	nblist_dis2_cutoff_XH () const

Real	nblist_dis2_cutoff_HH () const

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...

Real	lj_radius (int const i) const
	set these up in the ctor More...

Real	lj_wdepth (int const i) const

Real	lk_dgfree (int const i) const

Real	lk_volume (int const i) const

Real	lk_lambda (int const i) 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, but evaluate the function at the old grid points and then interpolate. 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_etable_derivatives (conformation::Atom const &at1, conformation::Atom const &at2, Real &dljatrE_ddis, Real &dljrepE_ddis, Real &dfasolE_ddis, Real &inv_d) const

Static Public Member Functions
static Real	eval_spline (Real const x, Real const xlo, Real const xhi, SplineParameters const &sp)

static Real	spline_deriv (Real const x, Real const xlo, Real const xhi, SplineParameters const &sp)

static Real	eval_spline (Real const x, Real const xlo, Real const xhi, Real const width, Real const invwidth, SplineParameters const &sp)

static Real	spline_deriv (Real const x, Real const xlo, Real const xhi, Real const width, Real const invwidth, SplineParameters const &sp)

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_spline_ramp_to_zero (Real const dis, EtableParamsOnePair const &p) const

Real	analytic_ljatr_spline_ramp_to_zero_deriv (Real const dis, EtableParamsOnePair const &p) const

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...

void	input_etable (ObjexxFCL::FArray3D< Real > &etable, const std::string label, std::istream &in)
	read in etable from a datafile More...

EtableParamsOnePair const &	analytic_params_for_pair (Size atype1, Size atype2) const

EtableParamsOnePair &	analytic_params_for_pair (Size atype1, Size atype2)

chemical::AtomType const &	atom_type (int const type)

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

bool const	lj_use_lj_deriv_slope

Real const	lj_slope_intercept

bool const	lj_use_hbond_radii

Real const	lj_hbond_OH_donor_dis

Real const	lj_hbond_dis

Real const	lj_hbond_hdis

Real const	lj_hbond_accOch_dis

Real const	lj_hbond_accOch_hdis

bool const	lj_use_water_radii

Real const	lj_water_dis

Real const	lj_water_hdis

Real const	lk_min_dis2sigma

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_

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	ljatr_spline_xlo
	Data needed to describe the splines for the ljatr term. More...

Real	ljatr_spline_xhi

Real	ljatr_spline_diff_xhi_xlo

Real	ljatr_spline_diff_xhi_xlo_inv

Real	fasol_spline_far_xlo
	Add extra repulsion, if desired, for certain atom pair interactions. More...

Real	fasol_spline_far_xhi

Real	fasol_spline_far_diff_xhi_xlo

Real	fasol_spline_far_diff_xhi_xlo_inv

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

Detailed Description

jk Class definition for Etable

Definition at line 164 of file Etable.hh.

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 83 of file Etable.cc.

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

constructor

Definition at line 89 of file Etable.cc.

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

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

Definition at line 899 of file Etable.hh.

References analytic_ljatr_spline_ramp_to_zero_deriv(), analytic_params_for_pair(), epsilon, core::scoring::etable::ExtraQuadraticRepulsion::extrapolated_slope, fasol_spline_far_diff_xhi_xlo, fasol_spline_far_diff_xhi_xlo_inv, fasol_spline_far_xhi, fasol_spline_far_xlo, lj_radius(), lk_inv_lambda2_, max_dis2, min_dis2, spline_deriv(), core::conformation::Atom::type(), and core::conformation::Atom::xyz().

Referenced by 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.

Definition at line 769 of file Etable.hh.

References analytic_lj_generic_form(), analytic_ljatr_spline_ramp_to_zero(), analytic_ljrep_linearized(), analytic_params_for_pair(), epsilon, eval_spline(), core::scoring::etable::ExtraQuadraticRepulsion::extrapolated_slope, fasol_spline_far_diff_xhi_xlo, fasol_spline_far_diff_xhi_xlo_inv, fasol_spline_far_xhi, fasol_spline_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_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_spline_xhi

Definition at line 1064 of file Etable.hh.

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

Referenced by analytic_etable_evaluation().

Real core::scoring::etable::Etable::analytic_ljatr_spline_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_spline_xlo < dis < p.ljatr_spline_xhi

Definition at line 1144 of file Etable.hh.

References eval_spline(), core::scoring::etable::EtableParamsOnePair::ljatr_spline_parameters, core::scoring::etable::EtableParamsOnePair::ljatr_spline_xhi, and core::scoring::etable::EtableParamsOnePair::ljatr_spline_xlo.

Referenced by analytic_etable_evaluation().

Real core::scoring::etable::Etable::analytic_ljatr_spline_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_spline_xlo < dis < p.ljatr_spline_xhi

Definition at line 1160 of file Etable.hh.

References core::scoring::etable::EtableParamsOnePair::ljatr_spline_parameters, core::scoring::etable::EtableParamsOnePair::ljatr_spline_xhi, core::scoring::etable::EtableParamsOnePair::ljatr_spline_xlo, and spline_deriv().

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.

Definition at line 1050 of file Etable.hh.

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().

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

inlineprivate

Definition at line 1172 of file Etable.hh.

References analytic_parameters, and n_atomtypes_.

Referenced by analytic_etable_derivatives(), analytic_etable_evaluation(), 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

Definition at line 1185 of file Etable.hh.

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

Definition at line 618 of file Etable.cc.

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

Definition at line 253 of file Etable.hh.

References atom_set_.

Referenced by core::scoring::etable::CoarseEtableEnergy::CoarseEtableEnergy(), core::scoring::methods::LK_BallEnergy::setup_d2_bounds(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::setup_for_derivatives(), core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::setup_for_scoring(), core::scoring::etable::TableLookupEtableEnergy::setup_for_scoring_(), and core::scoring::etable::AnalyticEtableEnergy::setup_for_scoring_().

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

inlineprivate

Definition at line 646 of file Etable.hh.

References atom_set_.

Referenced by make_pairenergy_table(), 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,
		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

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

calc_etable_value

Detailed:

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:

Authors: ctsa 10-2003

Last Modified:

Definition at line 1511 of file Etable.cc.

References epsilon, lj_radius(), lj_switch_dis2sigma, lk_min_dis2sigma, max_dis2, and min_dis2.

Referenced by make_pairenergy_table().

void core::scoring::etable::Etable::calculate_hydrogen_atom_reach ( )

private

Definition at line 294 of file Etable.cc.

References hydrogen_interaction_cutoff2_, 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

Definition at line 230 of file Etable.cc.

References 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

Definition at line 547 of file Etable.cc.

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

Definition at line 566 of file Etable.cc.

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)

Definition at line 143 of file Etable.cc.

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_, solv1_, and solv2_.

Referenced by Etable().

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

inline

const access to the deriv arrays

Definition at line 209 of file Etable.hh.

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

Definition at line 215 of file Etable.hh.

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

Definition at line 229 of file Etable.hh.

References dsolv_.

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

inline

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

Definition at line 222 of file Etable.hh.

References dsolv1_.

Real core::scoring::etable::Etable::eval_spline	(	Real const	x,
		Real const	xlo,
		Real const	xhi,
		SplineParameters const &	sp
	)

inlinestatic

Definition at line 1080 of file Etable.hh.

Referenced by analytic_etable_evaluation(), analytic_ljatr_spline_ramp_to_zero(), and core::scoring::hackelec::HackElecEnergy::eval_atom_atom_hack_elecE().

Real core::scoring::etable::Etable::eval_spline	(	Real const	x,
		Real const	xlo,
		Real const	xhi,
		Real const	width,
		Real const	invwidth,
		SplineParameters const &	sp
	)

inlinestatic

Definition at line 1108 of file Etable.hh.

References protocols::match::upstream::b, core::scoring::etable::SplineParameters::y2hi, core::scoring::etable::SplineParameters::y2lo, core::scoring::etable::SplineParameters::yhi, and core::scoring::etable::SplineParameters::ylo.

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

inline

Definition at line 247 of file Etable.hh.

References bins_per_A2.

Real core::scoring::etable::Etable::get_safe_max_dis2 ( ) const

inline

Definition at line 241 of file Etable.hh.

References safe_max_dis2.

Real core::scoring::etable::Etable::hydrogen_interaction_cutoff2 ( ) const

inline

Definition at line 259 of file Etable.hh.

References hydrogen_interaction_cutoff2_.

void core::scoring::etable::Etable::initialize_carbontypes_to_linearize_fasol ( )

private

Definition at line 310 of file Etable.cc.

References atom_set_, and carbon_types.

Referenced by Etable().

void core::scoring::etable::Etable::initialize_from_input_atomset ( chemical::AtomTypeSetCAP atom_set_in)

private

Definition at line 201 of file Etable.cc.

References atom_set_, lj_radius_, lj_wdepth_, lk_dgfree_, lk_lambda_, lk_volume_, max_hydrogen_lj_radius_, max_non_hydrogen_lj_radius_, and n_atomtypes_.

Referenced by Etable().

void core::scoring::etable::Etable::input_etable	(	ObjexxFCL::FArray3D< Real > &	etable,
		const std::string	label,
		std::istream &	in
	)

private

read in etable from a datafile

input_etable

Detailed:: $$$ file first line is <etable> <etable_disbins> $$$ 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:

Authors: sheffler mar 19 2006

Last Modified:

Definition at line 1194 of file Etable.cc.

References etable_disbins, and core::scoring::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, but evaluate the function at the old grid points and then interpolate. Useful for comparing the original etable evaluation with the analytic evaluation.

Definition at line 1706 of file Etable.cc.

References analytic_etable_evaluation(), bins_per_A2, and core::conformation::Atom::xyz().

Real core::scoring::etable::Etable::lj_radius ( int const i) const

inline

set these up in the ctor

Definition at line 313 of file Etable.hh.

References lj_radius_.

Referenced by analytic_etable_derivatives(), analytic_etable_evaluation(), calc_etable_value(), and precalc_etable_coefficients().

Real core::scoring::etable::Etable::lj_wdepth ( int const i) const

inline

Definition at line 320 of file Etable.hh.

References lj_wdepth_.

Referenced by precalc_etable_coefficients().

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

inline

const access to the arrays

Definition at line 184 of file Etable.hh.

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

Definition at line 190 of file Etable.hh.

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().

Real core::scoring::etable::Etable::lk_dgfree ( int const i) const

inline

Definition at line 327 of file Etable.hh.

References lk_dgfree_.

Referenced by precalc_etable_coefficients().

Real core::scoring::etable::Etable::lk_lambda ( int const i) const

inline

Definition at line 341 of file Etable.hh.

References lk_lambda_.

Referenced by precalc_etable_coefficients().

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

inline

Definition at line 334 of file Etable.hh.

References lk_volume_.

Referenced by precalc_etable_coefficients().

void core::scoring::etable::Etable::make_pairenergy_table ( )

private

calculate fast lookup arrays for vdw and solvation energy

Etable::make_pairenergy_table

Detailed:

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:

Authors: ctsa 10-2003

Last Modified:

Definition at line 352 of file Etable.cc.

Referenced by Etable().

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

inline

Definition at line 235 of file Etable.hh.

References max_dis_.

Referenced by core::scoring::methods::Fa_MbsolvEnergy::atomic_interaction_cutoff(), core::scoring::rna::RNA_LJ_BaseEnergy::atomic_interaction_cutoff(), core::scoring::methods::LK_hack::atomic_interaction_cutoff(), core::scoring::methods::LK_CosThetaEnergy::atomic_interaction_cutoff(), and core::scoring::methods::LK_BallEnergy::atomic_interaction_cutoff().

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

inline

Definition at line 265 of file Etable.hh.

References max_dis_.

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

inline

Definition at line 270 of file Etable.hh.

References max_heavy_hydrogen_cutoff_.

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

inline

Definition at line 275 of file Etable.hh.

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.

Definition at line 1701 of file Etable.cc.

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.

Definition at line 1693 of file Etable.cc.

References max_non_hydrogen_lj_radius_.

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

modify_pot

Detailed:: $$$ the Etables are modified in three ways: $$$ (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:

Authors: ctsa 10-2003

Last Modified:

Definition at line 728 of file Etable.cc.

Referenced by make_pairenergy_table().

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

inline

Definition at line 178 of file Etable.hh.

References n_atomtypes_.

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

Real core::scoring::etable::Etable::nblist_dis2_cutoff_HH ( ) const

inline

Definition at line 295 of file Etable.hh.

References nblist_dis2_cutoff_HH_.

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

inline

Definition at line 288 of file Etable.hh.

References nblist_dis2_cutoff_XH_.

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

inline

Definition at line 281 of file Etable.hh.

References nblist_dis2_cutoff_XX_.

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

private

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

output_etable

Detailed:: $$$ file first line is <etable> <etable_disbins> $$$ 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:

Authors: sheffler mar 19 2006

Last Modified:

Definition at line 1146 of file Etable.cc.

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

precalc_etable_coefficients

Detailed:

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:

Authors: ctsa 10-2003

Last Modified:

Definition at line 1289 of file Etable.cc.

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_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

Definition at line 247 of file Etable.cc.

References lj_radius_, lj_wdepth_, lk_dgfree_, lk_lambda_, lk_volume_, n_atomtypes_, and core::scoring::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

Definition at line 871 of file Etable.cc.

Referenced by make_pairenergy_table().

ObjexxFCL::FArray3D< Real > const& core::scoring::etable::Etable::solv1 ( ) const

inline

Definition at line 196 of file Etable.hh.

References solv1_.

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

inline

Definition at line 202 of file Etable.hh.

References solv2_.

Real core::scoring::etable::Etable::spline_deriv	(	Real const	x,
		Real const	xlo,
		Real const	xhi,
		SplineParameters const &	sp
	)

inlinestatic

Definition at line 1094 of file Etable.hh.

Referenced by analytic_etable_derivatives(), analytic_ljatr_spline_ramp_to_zero_deriv(), and core::scoring::hackelec::HackElecEnergy::eval_dhack_elecE_dr_over_r().

Real core::scoring::etable::Etable::spline_deriv	(	Real const	x,
		Real const	xlo,
		Real const	xhi,
		Real const	width,
		Real const	invwidth,
		SplineParameters const &	sp
	)

inlinestatic

Definition at line 1124 of file Etable.hh.

References protocols::match::upstream::b, core::scoring::etable::SplineParameters::y2hi, core::scoring::etable::SplineParameters::y2lo, core::scoring::etable::SplineParameters::yhi, and core::scoring::etable::SplineParameters::ylo.

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

Definition at line 1643 of file Etable.cc.

References analytic_params_for_pair(), atom_set_, atom_type(), bins_per_A2, dljatr(), etable_disbins, core::scoring::etable::EtableParamsOnePair::fasol_final_weight, core::scoring::etable::EtableParamsOnePair::hydrogen_interaction, 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

Definition at line 549 of file Etable.hh.

Referenced by calculate_normal_disbins(), and make_pairenergy_table().

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

private

Definition at line 640 of file Etable.hh.

Referenced by analytic_params_for_pair(), and dimension_etable_arrays().

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

private

Definition at line 521 of file Etable.hh.

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

Definition at line 528 of file Etable.hh.

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

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

private

Definition at line 635 of file Etable.hh.

Referenced by initialize_carbontypes_to_linearize_fasol(), core::scoring::etable::MembEtable::modify_pot(), and modify_pot_one_pair().

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

private

Definition at line 630 of file Etable.hh.

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

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

private

Definition at line 631 of file Etable.hh.

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

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

private

Definition at line 633 of file Etable.hh.

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

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

private

Definition at line 632 of file Etable.hh.

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

Real const core::scoring::etable::Etable::epsilon

private

Definition at line 551 of file Etable.hh.

Referenced by analytic_etable_derivatives(), analytic_etable_evaluation(), and calc_etable_value().

int const core::scoring::etable::Etable::etable_disbins

private

Definition at line 532 of file Etable.hh.

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

Real core::scoring::etable::Etable::fasol_spline_far_diff_xhi_xlo

private

Definition at line 604 of file Etable.hh.

Referenced by analytic_etable_derivatives(), analytic_etable_evaluation(), and smooth_etables_one_pair().

Real core::scoring::etable::Etable::fasol_spline_far_diff_xhi_xlo_inv

private

Definition at line 605 of file Etable.hh.

Referenced by analytic_etable_derivatives(), analytic_etable_evaluation(), and smooth_etables_one_pair().

Real core::scoring::etable::Etable::fasol_spline_far_xhi

private

Definition at line 603 of file Etable.hh.

Referenced by analytic_etable_derivatives(), analytic_etable_evaluation(), and smooth_etables_one_pair().

Real core::scoring::etable::Etable::fasol_spline_far_xlo

private

Add extra repulsion, if desired, for certain atom pair interactions.

Data needed to describe the splines for the fasol term: There are two splines 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" spline), and a second to smooth the transition where the distance goes to the fa_max_dis and the energy goes to 0 (the far spline). In between the close and far values, the exponential form of the energy function is used.

Definition at line 602 of file Etable.hh.

Referenced by analytic_etable_derivatives(), analytic_etable_evaluation(), and smooth_etables_one_pair().

Real core::scoring::etable::Etable::hydrogen_interaction_cutoff2_

private

Definition at line 553 of file Etable.hh.

Referenced by calculate_hydrogen_atom_reach(), and hydrogen_interaction_cutoff2().

Real const core::scoring::etable::Etable::lj_hbond_accOch_dis

private

Definition at line 541 of file Etable.hh.

Real const core::scoring::etable::Etable::lj_hbond_accOch_hdis

private

Definition at line 542 of file Etable.hh.

Real const core::scoring::etable::Etable::lj_hbond_dis

private

Definition at line 539 of file Etable.hh.

Referenced by precalc_etable_coefficients().

Real const core::scoring::etable::Etable::lj_hbond_hdis

private

Definition at line 540 of file Etable.hh.

Referenced by precalc_etable_coefficients().

Real const core::scoring::etable::Etable::lj_hbond_OH_donor_dis

private

Definition at line 538 of file Etable.hh.

Referenced by precalc_etable_coefficients().

ObjexxFCL::FArray2D< Real > core::scoring::etable::Etable::lj_r12_coeff_

private

Definition at line 569 of file Etable.hh.

Referenced by dimension_etable_arrays(), and make_pairenergy_table().

ObjexxFCL::FArray2D< Real > core::scoring::etable::Etable::lj_r6_coeff_

private

Definition at line 568 of file Etable.hh.

Referenced by dimension_etable_arrays(), and make_pairenergy_table().

utility::vector1< Real > core::scoring::etable::Etable::lj_radius_

private

Should the repulsive component start at ljatr+ljrep = 0 (true) or when ljatr reaches its minimum (false ) Data to turn off portions of the interactions between certain atom pairs e.g. Hydrogen atoms are repulsive, only, as are the REPLONLY atoms.

Definition at line 619 of file Etable.hh.

Referenced by dimension_etable_arrays(), initialize_from_input_atomset(), lj_radius(), and read_alternate_parameter_set().

ObjexxFCL::FArray2D< Real > core::scoring::etable::Etable::lj_sigma_

private

Definition at line 567 of file Etable.hh.

Referenced by dimension_etable_arrays(), and make_pairenergy_table().

Real const core::scoring::etable::Etable::lj_slope_intercept

private

Definition at line 536 of file Etable.hh.

Referenced by precalc_etable_coefficients().

Real const core::scoring::etable::Etable::lj_switch_dis2sigma

private

Definition at line 530 of file Etable.hh.

Referenced by calc_etable_value(), make_pairenergy_table(), and precalc_etable_coefficients().

ObjexxFCL::FArray2D< Real > core::scoring::etable::Etable::lj_switch_intercept_

private

Definition at line 570 of file Etable.hh.

Referenced by dimension_etable_arrays(), and make_pairenergy_table().

Real core::scoring::etable::Etable::lj_switch_sigma2dis

private

Definition at line 563 of file Etable.hh.

Referenced by make_pairenergy_table(), and precalc_etable_coefficients().

ObjexxFCL::FArray2D< Real > core::scoring::etable::Etable::lj_switch_slope_

private

Definition at line 571 of file Etable.hh.

Referenced by dimension_etable_arrays(), and make_pairenergy_table().

Real core::scoring::etable::Etable::lj_switch_slope_sigma2wdepth

private

Definition at line 565 of file Etable.hh.

Referenced by make_pairenergy_table(), and precalc_etable_coefficients().

Real core::scoring::etable::Etable::lj_switch_value2wdepth

private

Definition at line 564 of file Etable.hh.

Referenced by make_pairenergy_table(), and precalc_etable_coefficients().

bool const core::scoring::etable::Etable::lj_use_hbond_radii

private

Definition at line 537 of file Etable.hh.

Referenced by precalc_etable_coefficients().

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

private

Definition at line 535 of file Etable.hh.

Referenced by precalc_etable_coefficients().

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

private

Definition at line 543 of file Etable.hh.

Referenced by precalc_etable_coefficients().

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

private

Definition at line 544 of file Etable.hh.

Referenced by precalc_etable_coefficients().

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

private

Definition at line 545 of file Etable.hh.

Referenced by precalc_etable_coefficients().

utility::vector1< Real > core::scoring::etable::Etable::lj_wdepth_

private

Definition at line 620 of file Etable.hh.

Referenced by dimension_etable_arrays(), initialize_from_input_atomset(), lj_wdepth(), and read_alternate_parameter_set().

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

private

Definition at line 626 of file Etable.hh.

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

Real core::scoring::etable::Etable::ljatr_spline_diff_xhi_xlo

private

Definition at line 586 of file Etable.hh.

Real core::scoring::etable::Etable::ljatr_spline_diff_xhi_xlo_inv

private

Definition at line 587 of file Etable.hh.

Real core::scoring::etable::Etable::ljatr_spline_xhi

private

Definition at line 585 of file Etable.hh.

Real core::scoring::etable::Etable::ljatr_spline_xlo

private

Data needed to describe the splines for the ljatr term.

OK: these values reflect the grid point with the lowest energy, which could be different from the sum of the lj radii or the lj well depths. These vals define the switch point from attractive to repulsive. Repulsive interactions start counting at the lj_minima

Definition at line 584 of file Etable.hh.

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

private

Definition at line 627 of file Etable.hh.

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