Chemical Descriptors Library: Projected Molecule
Projected Molecule


Frequently, algorithms in graph theory are optimized for performance deleting vertices and/or edges that are not relevant for the calculation itself. Moreover, sometimes you are working with your molecule in the middle of a calculation of some property that calls, as a mid-step, other algorithm that uses vertex/edge deletion. Then you are faced with the question: if a pass the molecule as a reference, is a cheap call to the algorithm, but then the molecule gets modified, and I don't want this. Other solution would be to copy the molecule, and then pass the copy to the algorithm. This won't be convenient, since the copy of the molecule means the copy of all internal properties. If you're using customized props, and the props are lightweight, then this won't be an inconvenient. But when you're using default CDL props, or your own props which are heavy, this will involve in some overhead.
For this cases, other object is provided, which has as its properties, pointers to the properties of the molecule you are working on. Then the copy of the molecule will involve copying just one pointer per property: one pointer per atom and bond. When accessing a property of this 'projected molecule', then a pointer derreferenciation will be involved.
This object behaves almost as a molecule: the only difference is that it doesn't provide functions to add atoms and bonds, because where the pointers are going to point to?
An example says more than thousend words.

Suppose we want to get the vertices of the smallest set of smallest subrings, neatly organized in a vector of sets.
The SSSR algorithm of [Figueras] involves the deletion of vertices and edges. This algorithm is provided by CDL, and is documented somewhere else.
Here goes >10E3 words:

template<class Molecule>
std::vector<std::set<size_t> >
get_sssr_vertices(const Molecule& m) {

  // first some the objects needed to call the algorithm

  std::vector<std::set<size_t> >    cyclic_vertices;

  typename MolProperty<cyclic_edgesS,Molecule>::result_type&

  typename MolProperty<back_edgesS,Molecule>::result_type&

  // now the type we're interested in

  projected_molecule<Molecule>        proj_mol(m);
  return cyclic_vertices;


  1. Figueras, J.; "Ring Perception Using Breadth-First Search"; J.Chem.Inf.Comp.Sci. 1996, 36, 986-991.

Copyright © Vladimir Josef Sykora & Morphochem AG 2003
Copyright © Vladimir Josef Sykora 2003-2006