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include
BALL
SCORING
COMPONENTS
polarSolvation.h
Go to the documentation of this file.
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// $Id: polarSolvation.h,v 1.2 2006/05/21 17:49:46 anker Exp $
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#ifndef BALL_SCORING_COMPONENTS_POLARSOLVATION_H
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#define BALL_SCORING_COMPONENTS_POLARSOLVATION_H
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#include <
BALL/SCORING/COMMON/scoringComponent.h
>
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#include <
BALL/SOLVATION/poissonBoltzmann.h
>
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#include <
BALL/SOLVATION/generalizedBornCase.h
>
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namespace
BALL
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{
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class
PolarSolvation
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:
public
ScoringComponent
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{
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public
:
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enum
CalculationMethod
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{
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CALCULATION__FRESNO
,
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CALCULATION__FULL_SLICK
,
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CALCULATION__FULL_CYCLE
,
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CALCULATION__FULL_CYCLE_FOCUSED
,
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CALCULATION__COULOMB
,
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CALCULATION__EEF1
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};
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enum
AveragingMethod
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{
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AVERAGING__NONE
,
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AVERAGING__STATIC
,
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AVERAGING__RANDOM_FACTOR
,
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AVERAGING__RANDOM
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};
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struct
Option
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{
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static
const
char
*
POLAR_METHOD
;
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static
const
char
*
POLAR_GB
;
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static
const
char
*
POLAR_AVG
;
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static
const
char
*
POLAR_FOCUS_GRID_AROUND_LIGAND
;
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static
const
char
*
GB_SCALING_FILE
;
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static
const
char
*
UNITE_ATOMS
;
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static
const
char
*
VERBOSITY
;
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static
const
char
*
POLAR_OVERWRITE_RADII
;
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static
const
char
*
POLAR_OVERWRITE_CHARGES
;
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static
const
char
*
POLAR_RADIUS_RULES
;
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static
const
char
*
POLAR_CHARGE_RULES
;
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};
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struct
Default
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{
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static
const
Size
POLAR_METHOD
;
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static
const
bool
POLAR_GB
;
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static
const
Size
POLAR_AVG
;
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static
const
bool
POLAR_FOCUS_GRID_AROUND_LIGAND
;
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static
const
String
GB_SCALING_FILE
;
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static
const
bool
UNITE_ATOMS
;
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static
const
Size
VERBOSITY
;
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static
const
bool
POLAR_OVERWRITE_RADII
;
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static
const
bool
POLAR_OVERWRITE_CHARGES
;
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static
const
String
POLAR_RADIUS_RULES
;
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static
const
String
POLAR_CHARGE_RULES
;
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};
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PolarSolvation
()
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;
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PolarSolvation
(
ScoringFunction
& sf)
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;
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PolarSolvation
(
const
PolarSolvation
& fhb)
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;
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virtual
~PolarSolvation
()
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;
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const
PolarSolvation
&
operator =
(
const
PolarSolvation
& fr)
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;
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virtual
void
clear
()
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;
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bool
operator ==
(
const
PolarSolvation
& fr)
const
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;
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virtual
bool
setup
()
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;
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virtual
double
calculateScore
()
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;
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private
:
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/*_
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*/
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Molecule
desolv_protein_
;
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/*_
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*/
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Molecule
desolv_ligand_
;
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/*_
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*/
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Size
calculation_method_
;
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/*_
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*/
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Size
averaging_
;
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/*_
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*/
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bool
unite_atoms_
;
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/*_
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*/
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Size
verbosity_
;
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/*_
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*/
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FDPB
fdpb_
;
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/*_
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*/
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GeneralizedBornModel
gbm_
;
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/*_
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*/
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bool
use_gb_
;
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/*_
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*/
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float
spacing_
;
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/*_
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*/
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float
bulk_water_dc_
;
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/*_
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*/
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float
vacuum_dc_
;
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/*_
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*/
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bool
computeEnergyDifference_
(
System
& system,
float
& energy)
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;
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/*_
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*/
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bool
computeESEnergy_
(
System
& system,
float
& energy)
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;
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/*_
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*/
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float
computeESInteractionEnergy_
(
const
Molecule
& molecule,
const
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HashMap<const Atom*, float>
& p_hash)
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;
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/*_
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*/
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bool
computeFullCycle_
(
System
& system,
Molecule
& protein,
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Molecule
& ligand,
float
& energy)
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;
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/*_
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*/
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Vector3
permuteComponentSigns_
(
Vector3
vector,
Size
permutation)
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;
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/*_ Condense hydrogens without radius but bearing charges on the heavy
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atom they are attached to
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*/
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Size
uniteAtoms_
(
Molecule
& molecule)
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;
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};
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}
// namespace BALL
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#endif // BALL_SCORING_COMPONENTS_POLARSOLVATION_H
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