Scine::Swoose
2.1.0
This is the SCINE module Swoose.
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This class handles the generation of the connectivity of the molecular system. More...
#include <ConnectivityGenerator.h>
Public Member Functions | |
ConnectivityGenerator (ParametrizationData &data, std::shared_ptr< Utils::Settings > settings, Core::Log &log) | |
Constructor. | |
void | generateInitialListsOfNeighbors () |
This function generates the connectivity as a vector of lists of neighbor atom indices and updates the corresponding member in the ParametrizationData object. More... | |
void | refineListsOfNeighbors () |
Refines the connectivity based on information obtained from quantum-chemically calculated bond orders for fragments of the whole system. | |
This class handles the generation of the connectivity of the molecular system.
Right now: Bond detection with covalent radii. Possible in the future: PM6 or DFT bond orders, PDB parsing.
void Scine::MMParametrization::ConnectivityGenerator::generateInitialListsOfNeighbors | ( | ) |
This function generates the connectivity as a vector of lists of neighbor atom indices and updates the corresponding member in the ParametrizationData object.
The generated connectivity is just a guess and can be later refined after bond orders are obtained from quantum-chemical calculations of the fragments.