jk Class definition for Etable More...

#include <MembEtable.hh>

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

Collaboration diagram for core::scoring::etable::MembEtable:

Public Types
typedef Etable	Etable

typedef Etable	Etable

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

void	copy_from (Etable const *source)

ObjexxFCL::FArray3D< Real > const &	solv1 () const
	const access to the arrays More...

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

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

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

ObjexxFCL::FArray3D< Real > const &	dsolv1 () const
	const access to the deriv arrays 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
	pba More...

ObjexxFCL::FArray3D< Real > const &	memb_dsolv2 () const
	pba 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	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	lk_dgfree (int const i) const

Real	lk_volume (int const i) const

Real	lk_lambda (int const i) const

Real	memb_lk_dgfree (int const i) const

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

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

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

void	copy_from (Etable const *source)

ObjexxFCL::FArray3D< Real > const &	solv1 () const
	const access to the arrays More...

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

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

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

ObjexxFCL::FArray3D< Real > const &	dsolv1 () const
	const access to the deriv arrays 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
	pba More...

ObjexxFCL::FArray3D< Real > const &	memb_dsolv2 () const
	pba 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	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	lk_dgfree (int const i) const

Real	lk_volume (int const i) const

Real	lk_lambda (int const i) const

Real	memb_lk_dgfree (int const i) const

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

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

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

Private Member Functions
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...

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

void	smooth_etables ()

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

void	make_pairenergy_table ()
	calculate fast lookup arrays 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)

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)

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

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

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

void	smooth_etables ()

void	modify_pot ()

void	make_pairenergy_table ()

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)

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)

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_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 const	nblist_dis2_cutoff_XX_

Real const	nblist_dis2_cutoff_XH_

Real const	nblist_dis2_cutoff_HH_

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_dsolv2_

ObjexxFCL::FArray3D< Real >	memb_dsolv1_

Additional Inherited Members
Static Public Member Functions inherited from core::scoring::etable::Etable
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)

Detailed Description

jk Class definition for Etable

Definition at line 47 of file MembEtable.hh.

Member Typedef Documentation

typedef Etable core::scoring::etable::MembEtable::Etable

Definition at line 50 of file MembEtable.hh.

typedef Etable core::scoring::etable::MembEtable::Etable

Definition at line 53 of file MembEtable.hh.

Constructor & Destructor Documentation

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

constructor

Definition at line 59 of file MembEtable.cc.

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

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

constructor

Member Function Documentation

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

inline

Definition at line 161 of file MembEtable.hh.

References atom_set_.

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

inline

Definition at line 164 of file MembEtable.hh.

References atom_set_.

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

inlineprivate

Definition at line 363 of file MembEtable.hh.

References atom_set_.

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

inlineprivate

Definition at line 366 of file MembEtable.hh.

References atom_set_.

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

Referenced by make_pairenergy_table().

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

void core::scoring::etable::MembEtable::copy_from ( Etable const * source)

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

inline

const access to the deriv arrays

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

Definition at line 116 of file MembEtable.hh.

References dsolv1_.

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

inline

const access to the deriv arrays

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

Definition at line 119 of file MembEtable.hh.

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

Definition at line 123 of file MembEtable.hh.

References dsolv2_.

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

inline

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

Definition at line 126 of file MembEtable.hh.

References dsolv2_.

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

inline

Definition at line 155 of file MembEtable.hh.

References bins_per_A2.

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

inline

Definition at line 158 of file MembEtable.hh.

References bins_per_A2.

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

inline

Definition at line 149 of file MembEtable.hh.

References safe_max_dis2.

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

inline

Definition at line 152 of file MembEtable.hh.

References safe_max_dis2.

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

inline

Definition at line 167 of file MembEtable.hh.

References hydrogen_interaction_cutoff2_.

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

inline

Definition at line 170 of file MembEtable.hh.

References hydrogen_interaction_cutoff2_.

void core::scoring::etable::MembEtable::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 920 of file MembEtable.cc.

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

Referenced by make_pairenergy_table().

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

private

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

inline

set these up in the ctor

Definition at line 206 of file MembEtable.hh.

References lj_radius_.

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

inline

set these up in the ctor

Definition at line 209 of file MembEtable.hh.

References lj_radius_.

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

inline

Definition at line 220 of file MembEtable.hh.

References lk_dgfree_.

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

inline

Definition at line 223 of file MembEtable.hh.

References lk_dgfree_.

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

inline

Definition at line 254 of file MembEtable.hh.

References lk_dgrefce_.

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

inline

Definition at line 257 of file MembEtable.hh.

References lk_dgrefce_.

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

inline

Definition at line 234 of file MembEtable.hh.

References lk_lambda_.

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

inline

Definition at line 237 of file MembEtable.hh.

References lk_lambda_.

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

inline

Definition at line 227 of file MembEtable.hh.

References lk_volume_.

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

inline

Definition at line 230 of file MembEtable.hh.

References lk_volume_.

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

private

calculate fast lookup arrays for vdw and solvation energy

MembEtable::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 299 of file MembEtable.cc.

References add_long_range_damping, bins_per_A2, calc_etable_value(), dsolv1_, dsolv2_, etable_disbins, input_etable(), long_range_damping_length, max_dis2, max_dis_, memb_dsolv1_, memb_dsolv2_, memb_solv1_, memb_solv2_, modify_pot(), core::scoring::etable::Etable::n_atomtypes(), output_etable(), precalc_etable_coefficients(), smooth_etables(), solv1_, solv2_, and core::scoring::TR().

Referenced by MembEtable().

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

private

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

inline

Definition at line 143 of file MembEtable.hh.

References max_dis_.

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

inline

Definition at line 146 of file MembEtable.hh.

References max_dis_.

Real core::scoring::etable::MembEtable::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 1436 of file MembEtable.cc.

References max_hydrogen_lj_radius_.

Real core::scoring::etable::MembEtable::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.

Real core::scoring::etable::MembEtable::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 1428 of file MembEtable.cc.

References max_non_hydrogen_lj_radius_.

Real core::scoring::etable::MembEtable::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.

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

inline

pba

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

Definition at line 130 of file MembEtable.hh.

References memb_dsolv1_.

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

inline

pba

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

Definition at line 133 of file MembEtable.hh.

References memb_dsolv1_.

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

inline

pba

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

Definition at line 137 of file MembEtable.hh.

References memb_dsolv2_.

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

inline

pba

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

Definition at line 140 of file MembEtable.hh.

References memb_dsolv2_.

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

inline

Definition at line 241 of file MembEtable.hh.

References memb_lk_dgfree_.

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

inline

Definition at line 244 of file MembEtable.hh.

References memb_lk_dgfree_.

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

inline

Definition at line 267 of file MembEtable.hh.

References memb_lk_dgrefce_.

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

inline

Definition at line 270 of file MembEtable.hh.

References memb_lk_dgrefce_.

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

inline

Definition at line 89 of file MembEtable.hh.

References memb_solv1_.

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

inline

Definition at line 92 of file MembEtable.hh.

References memb_solv1_.

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

inline

Definition at line 96 of file MembEtable.hh.

References memb_solv2_.

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

inline

Definition at line 99 of file MembEtable.hh.

References memb_solv2_.

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

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)

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 587 of file MembEtable.cc.

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

Referenced by make_pairenergy_table().

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

private

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

inline

Definition at line 188 of file MembEtable.hh.

References nblist_dis2_cutoff_HH_.

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

inline

Definition at line 191 of file MembEtable.hh.

References nblist_dis2_cutoff_HH_.

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

inline

Definition at line 181 of file MembEtable.hh.

References nblist_dis2_cutoff_XH_.

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

inline

Definition at line 184 of file MembEtable.hh.

References nblist_dis2_cutoff_XH_.

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

inline

Definition at line 174 of file MembEtable.hh.

References nblist_dis2_cutoff_XX_.

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

inline

Definition at line 177 of file MembEtable.hh.

References nblist_dis2_cutoff_XX_.

void core::scoring::etable::MembEtable::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 872 of file MembEtable.cc.

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

Referenced by make_pairenergy_table().

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

private

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

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
	)