BALL
1.4.1
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#include <BALL/MOLMEC/AMBER/amber.h>
Classes | |
struct | Default |
struct | Option |
Public Member Functions | |
Constructors and Destructor | |
AmberFF () | |
AmberFF (System &system) | |
AmberFF (System &system, const Options &options) | |
AmberFF (const AmberFF &force_field) | |
virtual | ~AmberFF () |
Assignment | |
const AmberFF & | operator= (const AmberFF &force_field) |
virtual void | clear () |
Setup Methods | |
virtual bool | specificSetup () throw (Exception::TooManyErrors) |
Accessors specific to the AMBER force field | |
double | getStretchEnergy () const |
double | getBendEnergy () const |
double | getTorsionEnergy () const |
double | getNonbondedEnergy () const |
double | getESEnergy () const |
double | getVdWEnergy () const |
bool | hasInitializedParameters () const |
Size | getUpdateFrequency () const |
virtual String | getResults () const |
Get the current results in String form. | |
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ForceField () | |
ForceField (System &system) | |
ForceField (System &system, const Options &options) | |
ForceField (const ForceField &force_field) | |
virtual | ~ForceField () |
ForceField & | operator= (const ForceField &force_field) |
bool | isValid () const |
bool | setup (System &system) |
bool | setup (System &system, const Options &options) |
void | setMaximumNumberOfErrors (Size nr) |
Size | getMaximumNumberOfErrors () const |
HashSet< const Atom * > & | getUnassignedAtoms () |
Get the atoms, for which the force field setup failed. | |
void | setName (const String &name) |
String | getName () const |
Size | getNumberOfAtoms () const |
Size | getNumberOfMovableAtoms () const |
BALL_INLINE const AtomVector & | getAtoms () const |
BALL_INLINE System * | getSystem () |
BALL_INLINE const System * | getSystem () const |
BALL_INLINE bool | getUseSelection () const |
BALL_INLINE void | disableSelection () |
BALL_INLINE void | enableSelection () |
BALL_INLINE bool | isSelectionEnabled () const |
ForceFieldParameters & | getParameters () |
Size | countComponents () const |
const TimeStamp & | getUpdateTime () const |
const TimeStamp & | getSetupTime () const |
void | insertComponent (ForceFieldComponent *force_field_component) |
void | removeComponent (const ForceFieldComponent *force_field_component) |
void | removeComponent (const String &name) |
ForceFieldComponent * | getComponent (const Size index) const |
ForceFieldComponent * | getComponent (const String &name) const |
double | getEnergy () const |
double | updateEnergy () |
void | updateForces () |
double | getRMSGradient () const |
virtual void | update () throw (Exception::TooManyErrors) |
std::ostream & | error () throw (Exception::TooManyErrors) |
Protected Attributes | |
String | filename_ |
bool | parameters_initialized_ |
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System * | system_ |
AtomVector | atoms_ |
ForceFieldParameters | parameters_ |
bool | valid_ |
String | name_ |
double | energy_ |
vector< ForceFieldComponent * > | components_ |
Size | number_of_movable_atoms_ |
bool | use_selection_ |
bool | selection_enabled_ |
TimeStamp | update_time_stamp_ |
TimeStamp | setup_time_stamp_ |
HashSet< const Atom * > | unassigned_atoms_ |
Size | max_number_of_errors_ |
Size | number_of_errors_ |
Additional Inherited Members | |
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typedef std::vector< std::pair < Atom *, Atom * > > | PairVector |
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Options | options |
PeriodicBoundary | periodic_boundary |
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void | collectAtoms_ (const System &system) |
void | sortSelectedAtomVector_ () |
virtual void | performRequiredUpdates_ () |
BALL::AmberFF::AmberFF | ( | ) |
Default constructor.
BALL::AmberFF::AmberFF | ( | System & | system | ) |
Constructor.
BALL::AmberFF::AmberFF | ( | const AmberFF & | force_field | ) |
Copy constructor
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virtual |
Destructor.
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virtual |
Clear method
Reimplemented from BALL::ForceField.
double BALL::AmberFF::getBendEnergy | ( | ) | const |
Return the angle bend contribution to the total energy
double BALL::AmberFF::getESEnergy | ( | ) | const |
Return the electrostatic contribution to the total energy.
double BALL::AmberFF::getNonbondedEnergy | ( | ) | const |
Return the nonbonded contribution to the total energy. This energy comprises Van der Waals energy, hydrogen bond energy, and elesctrostatic energy.
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virtual |
Get the current results in String form.
Reimplemented from BALL::ForceField.
double BALL::AmberFF::getStretchEnergy | ( | ) | const |
Return the bond stretch contribution to the total energy
double BALL::AmberFF::getTorsionEnergy | ( | ) | const |
Return the torsion contribution to the total energy. This energy comprises proper and improper torsions.
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virtual |
Return the recommended number of iterations between updates. This method return 20 as a default value.
Reimplemented from BALL::ForceField.
double BALL::AmberFF::getVdWEnergy | ( | ) | const |
Return the Van der Waals and hydrogen bond contribution to the total energy.
bool BALL::AmberFF::hasInitializedParameters | ( | ) | const |
Return true, if the parameters have already been initialized
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virtual |
Force field specific setup
Reimplemented from BALL::ForceField.