| areInOneAromaticRing(const vector< Atom * > &v, Size ring_size=0) const (defined in MMFF94) | MMFF94 | |
| areInOneRing(vector< Atom * > v, Size ring_size=0) const (defined in MMFF94) | MMFF94 | |
| aromatic_bonds_ (defined in MMFF94) | MMFF94 | [protected] |
| aromatic_rings_ (defined in MMFF94) | MMFF94 | [protected] |
| assignBondTypes_() (defined in MMFF94) | MMFF94 | [protected] |
| assignMMFF94BondType(Bond &bond) const (defined in MMFF94) | MMFF94 | |
| atom_typer_ (defined in MMFF94) | MMFF94 | [protected] |
| atom_types_ (defined in MMFF94) | MMFF94 | [protected] |
| atoms_ (defined in ForceField) | ForceField | [protected] |
| bond_parameters_ (defined in MMFF94) | MMFF94 | [protected] |
| bonds_ (defined in MMFF94) | MMFF94 | [protected] |
| charge_processor_ (defined in MMFF94) | MMFF94 | [protected] |
| checkAtomType(Atom &atom) | MMFF94 | |
| clear() | MMFF94 | [virtual] |
| collectAtoms_(const System &system) (defined in ForceField) | ForceField | [protected] |
| collectBonds_() (defined in MMFF94) | MMFF94 | [protected] |
| collectRings_() (defined in MMFF94) | MMFF94 | [protected] |
| components_ (defined in ForceField) | ForceField | [protected] |
| countComponents() const | ForceField | |
| disableSelection() | ForceField | |
| enableSelection() | ForceField | |
| energy_ (defined in ForceField) | ForceField | [protected] |
| equivalences_ (defined in MMFF94) | MMFF94 | [protected] |
| error() (defined in ForceField) | ForceField | |
| es_parameters_ (defined in MMFF94) | MMFF94 | [protected] |
| folder_ (defined in MMFF94) | MMFF94 | [protected] |
| ForceField() | ForceField | |
| ForceField(System &system) | ForceField | |
| ForceField(System &system, const Options &options) | ForceField | |
| ForceField(const ForceField &force_field) | ForceField | |
| ForceFieldComponent (defined in ForceField) | ForceField | [friend] |
| getAromaticRings() const (defined in MMFF94) | MMFF94 | |
| getAtoms() const | ForceField | |
| getAtomTypes() const (defined in MMFF94) | MMFF94 | |
| getBendEnergy() const | MMFF94 | |
| getBonds() const (defined in MMFF94) | MMFF94 | |
| getComponent(const Size index) const | ForceField | |
| getComponent(const String &name) const | ForceField | |
| getEnergy() const | ForceField | |
| getEquivalences() const (defined in MMFF94) | MMFF94 | |
| getESEnergy() const | MMFF94 | |
| getMaximumNumberOfErrors() const | ForceField | |
| getName() const | ForceField | |
| getNonbondedEnergy() const | MMFF94 | |
| getNumberOfAtoms() const | ForceField | |
| getNumberOfMovableAtoms() const | ForceField | |
| getParameters() | ForceField | |
| getPlaneEnergy() const (defined in MMFF94) | MMFF94 | |
| getResults() const | MMFF94 | [virtual] |
| getRings() const (defined in MMFF94) | MMFF94 | |
| getRMSGradient() const | ForceField | |
| getSetupTime() const | ForceField | |
| getStretchBendEnergy() const (defined in MMFF94) | MMFF94 | |
| getStretchEnergy() const | MMFF94 | |
| getStretchParameters() const (defined in MMFF94) | MMFF94 | |
| getSystem() | ForceField | |
| getSystem() const | ForceField | |
| getTorsionEnergy() const | MMFF94 | |
| getUnassignedAtoms() | ForceField | |
| getUpdateFrequency() const | MMFF94 | [virtual] |
| getUpdateTime() const | ForceField | |
| getUseSelection() const | ForceField | |
| getVdWEnergy() const | MMFF94 | |
| hasInitializedParameters() const | MMFF94 | |
| insertComponent(ForceFieldComponent *force_field_component) | ForceField | |
| insertComponents_() (defined in MMFF94) | MMFF94 | [protected] |
| isInOneAromaticRing(const Bond &bond) const (defined in MMFF94) | MMFF94 | |
| isSelectionEnabled() const | ForceField | |
| isValid() const | ForceField | |
| kekuliser_ (defined in MMFF94) | MMFF94 | [protected] |
| max_number_of_errors_ (defined in ForceField) | ForceField | [protected] |
| MMFF94() | MMFF94 | |
| MMFF94(System &system) | MMFF94 | |
| MMFF94(System &system, const Options &options) | MMFF94 | |
| MMFF94(const MMFF94 &force_field) | MMFF94 | |
| name_ (defined in ForceField) | ForceField | [protected] |
| number_of_errors_ (defined in ForceField) | ForceField | [protected] |
| number_of_movable_atoms_ (defined in ForceField) | ForceField | [protected] |
| operator=(const MMFF94 &force_field) | MMFF94 | |
| ForceField::operator=(const ForceField &force_field) | ForceField | |
| options | ForceField | |
| PairVector typedef | ForceField | |
| parameters_ (defined in ForceField) | ForceField | [protected] |
| parameters_initialized_ (defined in MMFF94) | MMFF94 | [protected] |
| periodic_boundary | ForceField | |
| removeComponent(const ForceFieldComponent *force_field_component) | ForceField | |
| removeComponent(const String &name) | ForceField | |
| rings_ (defined in MMFF94) | MMFF94 | [protected] |
| selection_enabled_ (defined in ForceField) | ForceField | [protected] |
| setMaximumNumberOfErrors(Size nr) | ForceField | |
| setName(const String &name) | ForceField | |
| setup(System &system) | ForceField | |
| setup(System &system, const Options &options) | ForceField | |
| setup_time_stamp_ (defined in ForceField) | ForceField | [protected] |
| sortSelectedAtomVector_() (defined in ForceField) | ForceField | [protected] |
| specificSetup() | MMFF94 | [virtual] |
| system_ (defined in ForceField) | ForceField | [protected] |
| transformAromaticBonds_() (defined in MMFF94) | MMFF94 | [protected] |
| unassigned_atoms_ (defined in ForceField) | ForceField | [protected] |
| update() | ForceField | [virtual] |
| update_time_stamp_ (defined in ForceField) | ForceField | [protected] |
| updateEnergy() | ForceField | |
| updateForces() | ForceField | |
| use_selection_ (defined in ForceField) | ForceField | [protected] |
| valid_ (defined in ForceField) | ForceField | [protected] |
| ~ForceField() | ForceField | [virtual] |
| ~MMFF94() | MMFF94 | [virtual] |