Enumerations | |
Enums | |
| enum | PairListAlgorithmType { HASH_GRID, BRUTE_FORCE } |
Functions | |
| BALL_EXPORT BALL::Size | calculateNonBondedAtomPairs (ForceField::PairVector &pair_vector, const AtomVector &atom_vector, const SimpleBox3 &box, double distance, bool periodic_boundary_enabled, PairListAlgorithmType type) throw (Exception::OutOfMemory) |
| BALL_EXPORT Size | sortNonBondedAtomPairsAfterSelection (ForceField::PairVector &pair_vector) |
| BALL_EXPORT BALL::Size | addNonOverlappingMolecules (System &system, const HashGrid3< const Atom * > &solute_grid, const System &solvent, const SimpleBox3 &box, double distance) |
| BALL_EXPORT void | adaptWaterBox (System &system, const SimpleBox3 &box) |
| BALL_EXPORT void | calculateMinimumImage (Vector3 &distance, const Vector3 &period) |
| template<typename TorsionType , typename AtomIteratorType > | |
| Size | computeTorsions (const AtomIteratorType &start, const AtomIteratorType &end, std::vector< TorsionType > &torsions, bool use_selection=false) |
| BALL_EXPORT void BALL::MolmecSupport::adaptWaterBox | ( | System & | system, | |
| const SimpleBox3 & | box | |||
| ) |
Adapt periodic water (or general solvent) boxes to our periodic boundary definition. Periodic water boxes created by different programs might contain molecules which have their center of gravity outside of the box because of a different defintion of the periodic boundary. This function adapts such boxes to our definition by simply translating such molecules to the opposite boundary wall such that their center of gravity lies in the box afterwards.
| system | the system containing the water box which is to be adapted | |
| box | the box definition for the periodic boundary |
| BALL_EXPORT BALL::Size BALL::MolmecSupport::addNonOverlappingMolecules | ( | System & | system, | |
| const HashGrid3< const Atom * > & | solute_grid, | |||
| const System & | solvent, | |||
| const SimpleBox3 & | box, | |||
| double | distance | |||
| ) |
Merge the non-overlapping molecules of a system into another system. Fills system with copies of the solvent molecules stored in solvent. Solvent molecules are added to system if the molecules lie in the box and if they do not overlap with the molecules in solute_grid. A molecule has an overlap with another molecule if any atom of the first molecule is within distance of any atom of the other molecule.
| system | the system to be filled | |
| solute_grid | a hash grid containing the solute molecules | |
| solvent | the system containing the solvent | |
| box | the periodic boundary of system | |
| distance | used to determine overlaps between two atoms |
system | BALL_EXPORT void BALL::MolmecSupport::calculateMinimumImage | ( | Vector3 & | distance, | |
| const Vector3 & | period | |||
| ) |
Compute the minimum image
| BALL_EXPORT BALL::Size BALL::MolmecSupport::calculateNonBondedAtomPairs | ( | ForceField::PairVector & | pair_vector, | |
| const AtomVector & | atom_vector, | |||
| const SimpleBox3 & | box, | |||
| double | distance, | |||
| bool | periodic_boundary_enabled, | |||
| PairListAlgorithmType | type | |||
| ) | throw (Exception::OutOfMemory) |
Create a pair vector for non-bonded interactions. Calculates a vector of atom pairs whose distance is smaller than distance. The type determines if a brute force algorithm (type == BRUTE_FORCE) or a more sophisticated grid method (type == HASH_GRID) is used.
| pair_vector | the vector containing pairs of interacting atoms | |
| atom_vector | the atoms to be considered for pairs | |
| box | the periodic boundary used (if periodic_boundary_enabled == true) | |
| distance | the maximum distance (cut-off distance) for two atoms | |
| periodic_boundary_enabled | flag indicating the use of periodic boundary conditions | |
| type | the type of algorithm used to calculate the pair vector |
pair_vector.size()) | Size BALL::MolmecSupport::computeTorsions | ( | const AtomIteratorType & | start, | |
| const AtomIteratorType & | end, | |||
| std::vector< TorsionType > & | torsions, | |||
| bool | use_selection = false | |||
| ) | [inline] |
Compute all torsions in a given set of molecules.
torsions | start | an iterator pointing to the start of the atoms | |
| end | a past-the-end iterator for the atoms | |
| torsions | the vector of torsions | |
| use_selection | if set to true, a torsion will be added only if all four atoms are selected |
References BALL::Selectable::isSelected().
| BALL_EXPORT Size BALL::MolmecSupport::sortNonBondedAtomPairsAfterSelection | ( | ForceField::PairVector & | pair_vector | ) |
Sort the pair list. The atom pairs in the list ar sorted in such a way, that those atom pairs where at least one of the atoms is selected are at the beginning of the list. The number of such pairs is returned. Running time is linear in the length of the list.
| pair_vector | the unsorted pair_list (modified during the sorting) |