Scine::Swoose  2.0.0
This is the SCINE module Swoose.
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Scine::MMParametrization::ConnectivityGenerator Class Reference

This class handles the generation of the connectivity of the molecular system. More...

#include <ConnectivityGenerator.h>

Collaboration diagram for Scine::MMParametrization::ConnectivityGenerator:
Collaboration graph

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.
 

Detailed Description

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.

Member Function Documentation

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.

The documentation for this class was generated from the following files: