Table of pre-computed LK membrane solvation energies. More...

#include <MembEtable.hh>

Inheritance diagram for core::scoring::etable::MembEtable:

Public Member Functions
	MembEtable (chemical::AtomTypeSetCAP atom_set_in, EtableOptions const &options, std::string const &alternate_parameter_set="")

	MembEtable (MembEtable const &src)

	~MembEtable () override

ObjexxFCL::FArray3D< Real > const &	solv1 () const override
	Provide Constnat Access to Arrays. More...

ObjexxFCL::FArray3D< Real > const &	solv2 () const override

ObjexxFCL::FArray3D< Real > const &	memb_solv1 () const

ObjexxFCL::FArray3D< Real > const &	memb_solv2 () const

ObjexxFCL::FArray3D< Real > const &	dsolv1 () const override
	Return the solvation derivative table for the desolvation of atom1 by atom2. More...

ObjexxFCL::FArray3D< Real > const &	dsolv2 () const
	Return the solvation derivative table that combines atom1 and atom2's desolvations. More...

ObjexxFCL::FArray3D< Real > const &	memb_dsolv1 () const
	Return the solvation derivative table for the desolvation of atom1 by atom2. More...

ObjexxFCL::FArray3D< Real > const &	memb_dsolv2 () const
	return the solvation derivative table that combines atom1 and atom2's desolvations More...

virtual 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...

virtual 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 override
	set these up in the ctor More...

Real	lk_dgfree (int const i) const override
	Return the Lazardis Karplus DGFree value for an atom. More...

Real	lk_volume (int const i) const override
	Return the Lazaridis Karplus volume for an atom. More...

Real	lk_lambda (int const i) const override
	Return the Lazaridis Karplus "lambda" value (correlation distance) for an atom. More...

Real	memb_lk_dgfree (int const i) const

ObjexxFCL::FArray1D< Real > const &	lk_dgrefce () const

ObjexxFCL::FArray1D< Real > const &	memb_lk_dgrefce () const

void	output_etable (ObjexxFCL::FArray3D< Real > &etable, std::string label, std::ostream &out) override
	Output Etable: Output etable data in a file in the same format used in input. More...

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

Public Member Functions inherited from core::scoring::etable::Etable
	~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

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

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

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...

Real	lj_wdepth (int const i) const
	Return the Lennard-Jones well depth 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

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_memb_etable_arrays ()

void	initialize_from_atomset (chemical::AtomTypeSetCAP atom_set_in)

void	smooth_etables ()

void	modify_pot ()
	Modify Potential: Modify Etable to better treat 0-0, C-C, and H-H interactions. More...

void	make_pairenergy_table ()
	Make Pair Energy Table: Compute Fast Lookup for vdw and solvation energy. More...

void	precalc_etable_coefficients (ObjexxFCL::FArray2< Real > &lj_sigma, ObjexxFCL::FArray1< Real > &lk_inv_lambda2, ObjexxFCL::FArray2< Real > &lk_coeff, ObjexxFCL::FArray2< Real > &memb_lk_coeff, ObjexxFCL::FArray2< Real > &lk_min_dis2sigma_value, ObjexxFCL::FArray2< Real > &memb_lk_min_dis2sigma_value)
	precalculate non-distance dependent coefficients of energy functions More...

void	calc_etable_value (Real &dis2, int &atype1, int &atype2, Real &solvE1, Real &solvE2, Real &dsolvE1, Real &dsolvE2, ObjexxFCL::FArray2< Real > &lj_sigma, ObjexxFCL::FArray1< Real > &lk_inv_lambda2, ObjexxFCL::FArray2< Real > &lk_coeff, ObjexxFCL::FArray2< Real > &lk_min_dis2sigma_value, Real &memb_solvE1, Real &memb_solvE2, ObjexxFCL::FArray2< Real > &memb_lk_coeff, ObjexxFCL::FArray2< Real > &memb_lk_min_dis2sigma_value, Real &memb_dsolvE1, Real &memb_dsolvE2)
	calc all etable values given a distance and atom-type pair More...

Private Attributes
Real	max_non_hydrogen_lj_radius_

Real	max_hydrogen_lj_radius_

utility::vector1< Real >	lj_radius_

utility::vector1< Real >	lk_dgfree_

utility::vector1< Real >	lk_volume_

utility::vector1< Real >	lk_lambda_

utility::vector1< Real >	memb_lk_dgfree_

ObjexxFCL::FArray1D< Real >	lk_dgrefce_

ObjexxFCL::FArray1D< Real >	memb_lk_dgrefce_

ObjexxFCL::FArray3D< Real >	solv1_

ObjexxFCL::FArray3D< Real >	solv2_

ObjexxFCL::FArray3D< Real >	dsolv1_

ObjexxFCL::FArray3D< Real >	dsolv2_

ObjexxFCL::FArray3D< Real >	memb_solv1_

ObjexxFCL::FArray3D< Real >	memb_solv2_

ObjexxFCL::FArray3D< Real >	memb_dsolv1_

ObjexxFCL::FArray3D< Real >	memb_dsolv2_

Detailed Description

Table of pre-computed LK membrane solvation energies.

Constructor & Destructor Documentation

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

References dimension_memb_etable_arrays(), initialize_from_atomset(), and make_pairenergy_table().

core::scoring::etable::MembEtable::MembEtable ( MembEtable const & src )

core::scoring::etable::MembEtable::~MembEtable ( )

overridedefault

Member Function Documentation

void core::scoring::etable::MembEtable::calc_etable_value	(	Real &	dis2,
		int &	atype1,
		int &	atype2,
		Real &	solvE1,
		Real &	solvE2,
		Real &	dsolvE1,
		Real &	dsolvE2,
		ObjexxFCL::FArray2< Real > &	lj_sigma,
		ObjexxFCL::FArray1< Real > &	lk_inv_lambda2,
		ObjexxFCL::FArray2< Real > &	lk_coeff,
		ObjexxFCL::FArray2< Real > &	lk_min_dis2sigma_value,
		Real &	memb_solvE1,
		Real &	memb_solvE2,
		ObjexxFCL::FArray2< Real > &	memb_lk_coeff,
		ObjexxFCL::FArray2< Real > &	memb_lk_min_dis2sigma_value,
		Real &	memb_dsolvE1,
		Real &	memb_dsolvE2
	)

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

Author: ctsa (last modified: 10-2003)

References core::scoring::etable::Etable::epsilon(), lj_radius(), core::scoring::etable::Etable::lk_inv_lambda2(), core::scoring::etable::Etable::lk_min_dis2sigma(), core::scoring::etable::Etable::max_dis2(), and core::scoring::etable::Etable::min_dis2().

Referenced by make_pairenergy_table().

void core::scoring::etable::MembEtable::dimension_memb_etable_arrays ( )

private

References dsolv1_, dsolv2_, core::scoring::etable::Etable::etable_disbins(), lj_radius_, lk_dgfree_, lk_dgrefce_, lk_lambda_, lk_volume_, memb_dsolv1_, memb_dsolv2_, memb_lk_dgfree_, memb_lk_dgrefce_, memb_solv1_, memb_solv2_, core::scoring::etable::Etable::n_atomtypes(), solv1_, and solv2_.

Referenced by MembEtable().

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

inlineoverridevirtual

Return the solvation derivative table for the desolvation of atom1 by atom2.

Reimplemented from core::scoring::etable::Etable.

References dsolv1_.

ObjexxFCL::FArray3D< Real > const& core::scoring::etable::MembEtable::dsolv2 ( ) const

inline

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

References dsolv2_.

void core::scoring::etable::MembEtable::initialize_from_atomset ( chemical::AtomTypeSetCAP atom_set_in )

private

References lj_radius_, lk_dgfree_, lk_dgrefce_, lk_lambda_, lk_volume_, max_hydrogen_lj_radius_, max_non_hydrogen_lj_radius_, memb_lk_dgfree_, memb_lk_dgrefce_, core::scoring::etable::Etable::n_atomtypes(), and core::scoring::etable::TR().

Referenced by MembEtable().

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

overridevirtual

: Input Etable: read in etable from a datafile

file first line is <etable> <etable_disbins()> and other lines are <atom type 1> <atomtype 1> <eval bin 1> <eval bin 2>...

Author: sheffler (last modified: mar 19 2006)

Reimplemented from core::scoring::etable::Etable.

References core::scoring::etable::Etable::etable_disbins(), and core::scoring::etable::TR().

Referenced by make_pairenergy_table().

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

inlineoverridevirtual

set these up in the ctor

Reimplemented from core::scoring::etable::Etable.

References lj_radius_.

Referenced by calc_etable_value(), and precalc_etable_coefficients().

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

inlineoverridevirtual

Return the Lazardis Karplus DGFree value for an atom.

Reimplemented from core::scoring::etable::Etable.

References lk_dgfree_.

Referenced by precalc_etable_coefficients().

ObjexxFCL::FArray1D< Real > const& core::scoring::etable::MembEtable::lk_dgrefce ( ) const

inline

References lk_dgrefce_.

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

inlineoverridevirtual

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

Reimplemented from core::scoring::etable::Etable.

References lk_lambda_.

Referenced by precalc_etable_coefficients().

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

inlineoverridevirtual

Return the Lazaridis Karplus volume for an atom.

Reimplemented from core::scoring::etable::Etable.

References lk_volume_.

Referenced by precalc_etable_coefficients().

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

private

Make Pair Energy Table: Compute Fast Lookup 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.

Author: ctsa (last modified: 10-2003)

Referenced by MembEtable().

virtual Real core::scoring::etable::MembEtable::max_hydrogen_lj_radius ( ) const

inlinevirtual

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_.

virtual Real core::scoring::etable::MembEtable::max_non_hydrogen_lj_radius ( ) const

inlinevirtual

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_.

ObjexxFCL::FArray3D< Real > const& core::scoring::etable::MembEtable::memb_dsolv1 ( ) const

inline

Return the solvation derivative table for the desolvation of atom1 by atom2.

References memb_dsolv1_.

ObjexxFCL::FArray3D< Real > const& core::scoring::etable::MembEtable::memb_dsolv2 ( ) const

inline

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

References memb_dsolv2_.

Real core::scoring::etable::MembEtable::memb_lk_dgfree ( int const i ) const

inline

References memb_lk_dgfree_.

Referenced by precalc_etable_coefficients().

ObjexxFCL::FArray1D< Real > const& core::scoring::etable::MembEtable::memb_lk_dgrefce ( ) const

inline

References memb_lk_dgrefce_.

ObjexxFCL::FArray3D< Real > const& core::scoring::etable::MembEtable::memb_solv1 ( ) const

inline

References memb_solv1_.

ObjexxFCL::FArray3D< Real > const& core::scoring::etable::MembEtable::memb_solv2 ( ) const

inline

References memb_solv2_.

void core::scoring::etable::MembEtable::modify_pot ( )

private

Modify Potential: 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)

Author: ctsa (last modified: 10-2003)

References core::scoring::etable::Etable::atom_set(), core::pack::dunbrack::c, dsolv1_, dsolv2_, core::scoring::etable::Etable::etable_disbins(), memb_dsolv1_, memb_dsolv2_, memb_solv1_, memb_solv2_, solv1_, solv2_, and core::scoring::etable::TR().

Referenced by make_pairenergy_table().

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

overridevirtual

Output Etable: Output etable data in a file in the same format used in input.

File first line is <etable> <etable_disbins()> and other lines are <atom type 1> <atomtype 1> <eval bin 1> <eval bin 2>...

Author: sheffler (last modified: mar 19 2006)

Reimplemented from core::scoring::etable::Etable.

References core::scoring::etable::Etable::etable_disbins(), and core::scoring::etable::Etable::n_atomtypes().

Referenced by make_pairenergy_table().

void core::scoring::etable::MembEtable::precalc_etable_coefficients	(	ObjexxFCL::FArray2< Real > &	lj_sigma,
		ObjexxFCL::FArray1< Real > &	lk_inv_lambda2,
		ObjexxFCL::FArray2< Real > &	lk_coeff,
		ObjexxFCL::FArray2< Real > &	memb_lk_coeff,
		ObjexxFCL::FArray2< Real > &	lk_min_dis2sigma_value,
		ObjexxFCL::FArray2< Real > &	memb_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