BALL::MMFF94 Class Reference
[MMFF94 Force
Field.]
MMFF94 force field class.
More...
#include <MMFF94.h>
Inheritance diagram for BALL::MMFF94:
[legend]
Classes |
|
| struct | Default |
| Default values for
MMFF94 options. More... |
|
| struct | Option |
| Option names. More... |
|
Public Member Functions |
|
|
Constructors and Destructor
|
|
| MMFF94 () | |
| Default
constructor. |
|
| MMFF94 (System &system) | |
| Constructor. |
|
| MMFF94 (System &system, const Options &options) | |
| Constructor. |
|
| MMFF94 (const MMFF94 &force_field) | |
| Copy constructor. |
|
| virtual | ~MMFF94 () |
| Destructor. |
|
|
Assignment
|
|
| const MMFF94 & | operator= (const MMFF94 &force_field) |
| Assignment operator. |
|
| virtual void | clear () |
| Clear method. |
|
|
Setup Methods
|
|
| virtual bool | specificSetup () throw (Exception::TooManyErrors) |
| Force field specific
setup. |
|
|
Accessors specific to the MMFF94 force field
|
|
| double | getStretchEnergy () const |
| Return the bond stretch contribution
to the total energy. |
|
| double | getBendEnergy () const |
| Return the angle bend contribution
to the total energy. |
|
| double | getStretchBendEnergy () const |
| double | getTorsionEnergy () const |
| Return the torsion contribution to
the total energy. |
|
| double | getNonbondedEnergy () const |
| Return the nonbonded contribution to
the total energy. |
|
| double | getESEnergy () const |
| Return the electrostatic
contribution to the total energy. |
|
| double | getVdWEnergy () const |
| Return the Van der Waals and
hydrogen bond contribution to the total energy. |
|
| double | getPlaneEnergy () const |
| bool | hasInitializedParameters () const |
| Return true, if the parameters have
already been initialized. |
|
| Size | getUpdateFrequency () const |
| Return the recommended number of
iterations between updates. |
|
| virtual String | getResults () const |
| Get the current results in String form. |
|
| const vector< Bond * > | getBonds () const |
| const vector< HashSet< Atom * > > & | getRings () const |
| const vector< HashSet< Atom * > > & | getAromaticRings () const |
| bool | isInOneAromaticRing (const Bond &bond) const |
| bool | assignMMFF94BondType (Bond &bond) const |
| const vector< MMFF94AtomType > & | getAtomTypes () const |
| const MMFF94StretchParameters & | getStretchParameters () const |
| const MMFF94AtomTypeEquivalences & | getEquivalences () const |
| bool | areInOneRing (vector< Atom * > v, Size ring_size=0) const |
| bool | areInOneAromaticRing (const vector< Atom * > &v, Size ring_size=0) const |
| bool | checkAtomType (Atom &atom) |
| Check wheter the atoms type is
valid. |
|
Protected Member Functions |
|
| void | insertComponents_ () |
| void | transformAromaticBonds_ () |
| void | collectBonds_ () |
| void | assignBondTypes_ () |
| void | collectRings_ () |
Protected Attributes |
|
| String | folder_ |
| MMFF94AtomTypes | atom_types_ |
| MMFF94StretchParameters | bond_parameters_ |
| MMFF94AtomTypeEquivalences | equivalences_ |
| MMFF94ESParameters | es_parameters_ |
| vector< HashSet< Atom * > > | rings_ |
| vector< HashSet< Atom * > > | aromatic_rings_ |
| bool | parameters_initialized_ |
| vector< Bond * > | bonds_ |
| MMFF94AtomTyper | atom_typer_ |
| MMFF94ChargeProcessor | charge_processor_ |
| Kekuliser | kekuliser_ |
| HashSet< Bond * > | aromatic_bonds_ |
Detailed Description
MMFF94 force field class.Member Function Documentation
| bool BALL::MMFF94::checkAtomType | ( | Atom & | atom | ) |
Check wheter the atoms type is valid.
If not, add it to unassigned atoms.
| double BALL::MMFF94::getNonbondedEnergy | ( | ) | const |
Return the nonbonded contribution to the total energy.
This energy comprises Van der Waals energy, hydrogen bond energy, and elesctrostatic energy.
| double BALL::MMFF94::getTorsionEnergy | ( | ) | const |
Return the torsion contribution to the total energy.
This energy comprises proper and improper torsions.
| Size BALL::MMFF94::getUpdateFrequency | ( | ) | const [virtual] |
Return the recommended number of iterations between updates.
This method return 20 as a default value.
Reimplemented from BALL::ForceField.
