BALL::PolarSolvation Class Reference
#include <BALL/SCORING/COMPONENTS/polarSolvation.h>
List of all members.
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Classes |
struct | Default |
struct | Option |
Public Types |
enum | CalculationMethod {
CALCULATION__FRESNO,
CALCULATION__FULL_SLICK,
CALCULATION__FULL_CYCLE,
CALCULATION__FULL_CYCLE_FOCUSED,
CALCULATION__COULOMB,
CALCULATION__EEF1
} |
enum | AveragingMethod { AVERAGING__NONE,
AVERAGING__STATIC,
AVERAGING__RANDOM_FACTOR,
AVERAGING__RANDOM
} |
Public Member Functions |
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| PolarSolvation () |
| PolarSolvation (ScoringFunction &sf) |
| PolarSolvation (const PolarSolvation &fhb) |
virtual | ~PolarSolvation () |
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const PolarSolvation & | operator= (const PolarSolvation &fr) |
virtual void | clear () |
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bool | operator== (const PolarSolvation &fr) const |
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virtual bool | setup () |
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virtual double | calculateScore () |
Private Member Functions |
bool | computeEnergyDifference_ (System &system, float &energy) |
bool | computeESEnergy_ (System &system, float &energy) |
float | computeESInteractionEnergy_ (const Molecule &molecule, const HashMap< const Atom *, float > &p_hash) |
bool | computeFullCycle_ (System &system, Molecule &protein, Molecule &ligand, float &energy) |
Vector3 | permuteComponentSigns_ (Vector3 vector, Size permutation) |
Size | uniteAtoms_ (Molecule &molecule) |
Private Attributes |
Molecule | desolv_protein_ |
Molecule | desolv_ligand_ |
Size | calculation_method_ |
Size | averaging_ |
bool | unite_atoms_ |
Size | verbosity_ |
FDPB | fdpb_ |
GeneralizedBornModel | gbm_ |
bool | use_gb_ |
float | spacing_ |
float | bulk_water_dc_ |
float | vacuum_dc_ |
Detailed Description
SLICK polar solvation component \ { Definition:} {BALL/SCORING/COMPONENTS/polarSolvation.h}
Member Enumeration Documentation
Averaging methods for model 0 and 3
- Enumerator:
AVERAGING__NONE |
No averaging will be done.
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AVERAGING__STATIC |
The grid of the PB solver will be translated a bit in every direction by a fixed length.
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AVERAGING__RANDOM_FACTOR |
The grid of the PB solver will be translated a bit in every direction by a randomly chosen length (not yet implemented).
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AVERAGING__RANDOM |
The grid of the PB solver will be translated a bit in every direction by different randomly chosen length (not yet implemented).
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- Enumerator:
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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Constructor & Destructor Documentation
BALL::PolarSolvation::PolarSolvation |
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virtual BALL::PolarSolvation::~PolarSolvation |
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[virtual] |
Member Function Documentation
virtual double BALL::PolarSolvation::calculateScore |
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[virtual] |
virtual void BALL::PolarSolvation::clear |
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[virtual] |
bool BALL::PolarSolvation::computeEnergyDifference_ |
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System & |
system, |
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float & |
energy | |
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bool BALL::PolarSolvation::computeESEnergy_ |
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System & |
system, |
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float & |
energy | |
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Vector3 BALL::PolarSolvation::permuteComponentSigns_ |
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Vector3 |
vector, |
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Size |
permutation | |
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virtual bool BALL::PolarSolvation::setup |
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[virtual] |
Size BALL::PolarSolvation::uniteAtoms_ |
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Molecule & |
molecule |
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[private] |
Member Data Documentation