Rosetta Core  2014.35
Public Types | Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::scoring::etable::MembEtable Class Reference

jk Class definition for Etable More...

#include <MembEtable.hh>

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="")
 Construct Membrane Etable. More...
 
void copy_from (Etable const *source)
 
ObjexxFCL::FArray3D< Real > const & solv1 () const
 Provide Constnat Access to 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
 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...
 
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
 The 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...
 
Real nblist_dis2_cutoff_XH () const
 The 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...
 
Real nblist_dis2_cutoff_HH () const
 The 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_radius (int const i) const
 Return the Lennard-Jones radius for an atom. More...
 
Real lj_wdepth (int const i) const
 Return the Lennard-Jones well depth for an atom. More...
 
Real lk_dgfree (int const i) const
 Return the Lazardis Karplus DGFree value for an atom. More...
 
Real lk_volume (int const i) const
 Return the Lazaridis Karplus volume for an atom. More...
 
Real lk_lambda (int const i) const
 Return the Lazaridis Karplus "lambda" value (correlation distance) for an atom. More...
 
Real lk_inv_lambda2 (int const i) const
 
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
 

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)
 Get Atom Type corresponding to index. More...
 
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< Reallj_radius_
 
utility::vector1< Reallk_dgfree_
 
utility::vector1< Reallk_volume_
 
utility::vector1< Reallk_lambda_
 
utility::vector1< Realmemb_lk_dgfree_
 
ObjexxFCL::FArray1D< Reallk_dgrefce_
 
ObjexxFCL::FArray1D< Realmemb_lk_dgrefce_
 
ObjexxFCL::FArray3D< Realsolv1_
 
ObjexxFCL::FArray3D< Realsolv2_
 
ObjexxFCL::FArray3D< Realdsolv1_
 
ObjexxFCL::FArray3D< Realdsolv2_
 
ObjexxFCL::FArray3D< Realmemb_solv1_
 
ObjexxFCL::FArray3D< Realmemb_solv2_
 
ObjexxFCL::FArray3D< Realmemb_dsolv2_
 
ObjexxFCL::FArray3D< Realmemb_dsolv1_
 

Additional Inherited Members

- Static Public Member Functions inherited from core::scoring::etable::Etable
static CubicPolynomial cubic_polynomial_from_spline (Real xlo, Real xhi, SplineParameters const &sp)
 
static Real eval_cubic_polynomial (Real const x, CubicPolynomial const &sp)
 
static Real cubic_polynomial_deriv (Real const x, CubicPolynomial const &cp)
 

Detailed Description

jk Class definition for Etable

Class for Definition of a Membrane Protein Specific Etable.

Member Typedef Documentation

Constructor & Destructor Documentation

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

Construct Membrane Etable.

Construct membrane etable from an atom typeset, generic set of etable options and alternate parameter set

Member Function Documentation

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

References atom_set_.

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

References atom_set_.

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

Get Atom Type corresponding to index.

References atom_set_.

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

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
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::copy_from ( Etable const *  source)
void core::scoring::etable::MembEtable::copy_from ( Etable const *  source)
ObjexxFCL::FArray3D< Real > const& core::scoring::etable::MembEtable::dsolv1 ( ) const
inline

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

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

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_.

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_.

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

References bins_per_A2.

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

References bins_per_A2.

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

References safe_max_dis2.

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

References safe_max_dis2.

Real core::scoring::etable::MembEtable::hydrogen_interaction_cutoff2 ( ) const
inline
Real core::scoring::etable::MembEtable::hydrogen_interaction_cutoff2 ( ) const
inline
void core::scoring::etable::MembEtable::input_etable ( ObjexxFCL::FArray3D< Real > &  etable,
const std::string  label,
std::istream &  in 
)
private
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: 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:

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)
Last Modified:

References bin, etable_disbins, core::scoring::TR, and utility_exit_with_message.

Referenced by make_pairenergy_table().

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

set these up in the ctor

References lj_radius_.

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

set these up in the ctor

References lj_radius_.

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

References lk_dgfree_.

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

References lk_dgfree_.

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

References lk_dgrefce_.

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
inline

References lk_lambda_.

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

References lk_lambda_.

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

References lk_volume_.

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

References lk_volume_.

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

calculate fast lookup arrays for vdw and solvation energy

Make Pair Energy Table: Compute Fast Lookup 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:

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)

References add_long_range_damping, bins_per_A2, calc_etable_value(), dsolv1_, dsolv2_, etable_disbins, input_etable(), score::input_etables, core::scoring::etable::Etable::lk_inv_lambda2(), long_range_damping_length, max_dis2, max_dis_, memb_dsolv1_, memb_dsolv2_, memb_solv1_, memb_solv2_, modify_pot(), core::scoring::etable::Etable::n_atomtypes(), score::no_smooth_etables, option, out, output_etable(), score::output_etables, precalc_etable_coefficients(), smooth_etables(), solv1_, solv2_, tag, core::scoring::TR, and user.

Referenced by MembEtable().

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

References max_dis_.

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

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.

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.

References max_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.

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.

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_dsolv1 ( ) const
inline

pba

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_.

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

References memb_dsolv2_.

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

References memb_lk_dgfree_.

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

References memb_lk_dgfree_.

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

References memb_lk_dgrefce_.

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_solv1 ( ) const
inline

References memb_solv1_.

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

References memb_solv2_.

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

References memb_solv2_.

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

modify Etable to better treat 0-0, C-C, and H-H interactions

Modify Potential: 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:

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

Referenced by make_pairenergy_table().

Real core::scoring::etable::MembEtable::nblist_dis2_cutoff_HH ( ) const
inline
Real core::scoring::etable::MembEtable::nblist_dis2_cutoff_HH ( ) const
inline
Real core::scoring::etable::MembEtable::nblist_dis2_cutoff_XH ( ) const
inline
Real core::scoring::etable::MembEtable::nblist_dis2_cutoff_XH ( ) const
inline
Real core::scoring::etable::MembEtable::nblist_dis2_cutoff_XX ( ) const
inline
Real core::scoring::etable::MembEtable::nblist_dis2_cutoff_XX ( ) const
inline
void core::scoring::etable::MembEtable::output_etable ( ObjexxFCL::FArray3D< Real > &  etable,
std::string  label,
std::ostream &  out 
)
private
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: Output etable data in a file in the same format used in input.

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:

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)

References bin, 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
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::smooth_etables ( )
private
void core::scoring::etable::MembEtable::smooth_etables ( )
private
ObjexxFCL::FArray3D< Real > const& core::scoring::etable::MembEtable::solv1 ( ) const
inline

Provide Constnat Access to Arrays.

References solv1_.

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

const access to the arrays

References solv1_.

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

References solv2_.

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

References solv2_.

Member Data Documentation

bool const core::scoring::etable::MembEtable::add_long_range_damping
private

Referenced by make_pairenergy_table().

chemical::AtomTypeSetCAP core::scoring::etable::MembEtable::atom_set_
private

Referenced by atom_set(), atom_type(), and modify_pot().

int const core::scoring::etable::MembEtable::bins_per_A2
private
ObjexxFCL::FArray3D< Real > core::scoring::etable::MembEtable::dsolv1_
private
ObjexxFCL::FArray3D< Real > core::scoring::etable::MembEtable::dsolv2_
private
Real const core::scoring::etable::MembEtable::epsilon
private
int const core::scoring::etable::MembEtable::etable_disbins
private
Real core::scoring::etable::MembEtable::hydrogen_interaction_cutoff2_
private
Real const core::scoring::etable::MembEtable::lj_hbond_accOch_dis
private
Real const core::scoring::etable::MembEtable::lj_hbond_accOch_hdis
private
Real const core::scoring::etable::MembEtable::lj_hbond_dis
private
Real const core::scoring::etable::MembEtable::lj_hbond_hdis
private
utility::vector1< Real > core::scoring::etable::MembEtable::lj_radius_
private

Referenced by lj_radius(), and MembEtable().

Real const core::scoring::etable::MembEtable::lj_slope_intercept
private
Real const core::scoring::etable::MembEtable::lj_switch_dis2sigma
private
bool const core::scoring::etable::MembEtable::lj_use_hbond_radii
private
bool const core::scoring::etable::MembEtable::lj_use_lj_deriv_slope
private
bool const core::scoring::etable::MembEtable::lj_use_water_radii
private
Real const core::scoring::etable::MembEtable::lj_water_dis
private
Real const core::scoring::etable::MembEtable::lj_water_hdis
private
utility::vector1< Real > core::scoring::etable::MembEtable::lk_dgfree_
private

Referenced by lk_dgfree(), and MembEtable().

ObjexxFCL::FArray1D< Real > core::scoring::etable::MembEtable::lk_dgrefce_
private

Referenced by lk_dgrefce(), and MembEtable().

utility::vector1< Real > core::scoring::etable::MembEtable::lk_lambda_
private

Referenced by lk_lambda(), and MembEtable().

Real const core::scoring::etable::MembEtable::lk_min_dis2sigma
private
utility::vector1< Real > core::scoring::etable::MembEtable::lk_volume_
private

Referenced by lk_volume(), and MembEtable().

Real const core::scoring::etable::MembEtable::long_range_damping_length
private

Referenced by make_pairenergy_table().

Real const core::scoring::etable::MembEtable::max_dis2
private

Referenced by make_pairenergy_table().

Real const core::scoring::etable::MembEtable::max_dis_
private
Real core::scoring::etable::MembEtable::max_hydrogen_lj_radius_
private
Real core::scoring::etable::MembEtable::max_non_hydrogen_lj_radius_
private
ObjexxFCL::FArray3D< Real > core::scoring::etable::MembEtable::memb_dsolv1_
private
ObjexxFCL::FArray3D< Real > core::scoring::etable::MembEtable::memb_dsolv2_
private
utility::vector1< Real > core::scoring::etable::MembEtable::memb_lk_dgfree_
private

Referenced by memb_lk_dgfree(), and MembEtable().

ObjexxFCL::FArray1D< Real > core::scoring::etable::MembEtable::memb_lk_dgrefce_
private

Referenced by memb_lk_dgrefce(), and MembEtable().

ObjexxFCL::FArray3D< Real > core::scoring::etable::MembEtable::memb_solv1_
private
ObjexxFCL::FArray3D< Real > core::scoring::etable::MembEtable::memb_solv2_
private
Real const core::scoring::etable::MembEtable::min_dis
private
Real const core::scoring::etable::MembEtable::min_dis2
private
int const core::scoring::etable::MembEtable::n_atomtypes
private
Real const core::scoring::etable::MembEtable::nblist_dis2_cutoff_HH_
private

Referenced by nblist_dis2_cutoff_HH().

Real const core::scoring::etable::MembEtable::nblist_dis2_cutoff_XH_
private

Referenced by nblist_dis2_cutoff_XH().

Real const core::scoring::etable::MembEtable::nblist_dis2_cutoff_XX_
private

Referenced by nblist_dis2_cutoff_XX().

Real const core::scoring::etable::MembEtable::safe_max_dis2
private

Referenced by get_safe_max_dis2().

ObjexxFCL::FArray3D< Real > core::scoring::etable::MembEtable::solv1_
private
ObjexxFCL::FArray3D< Real > core::scoring::etable::MembEtable::solv2_
private
Real const core::scoring::etable::MembEtable::Wradius
private

The documentation for this class was generated from the following files: