Volume 1 Chapter 7 Composite Geometric Parameters

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7.6 Numerical Limits for the 3D Search

Having defined the parameters which, we think, best describe the spatial feature(s) of a fragment, the 3D search process itself is deceptively simple: we specify limiting numerical values for one or more of the parameters so as to generate hit-fragments that correspond to the desired geometrical subset.

The 3D search constraints can be applied in three ways:

(i)
By simply specifying the range of values which a parameter may have for the fragment to be registered as a hit.

To implement this we use the SELECT command.

Thus in the morphine example we defined: DIST X1 6

and later SELECTed DIST as: DIST 4.45 4.75

(ii)
By defining a sphere of inclusion of radius r about a point P in the fragment.

If any atom lies within this sphere then the crystal fragment will be accepted by the search process and, subject to it passing all other constraints, a hit will be registered.

(iii)
By defining a sphere of exclusion of radius r about a point P in the fragment.

If any atom lies within this sphere then the crystal fragment will be rejected by the search process and no hit will be registered.

In organic chemistry, the spheres of inclusion/exclusion are equivalent to the location of fragments with sterically hindered (or sterically non-hindered) environments at a particular site. In this context, these new 3D constraints add considerably to the facilities for restricting the fragment environment, as embodied in 2D searching using the NOLN and NOCR instructions described in chapter 6.

In molecular modelling and molecular design, it may be important to know whether a non-atomic point (centroid or dummy atom) is hindered or not, and the sphere of inclusion/exclusion facilities of QUEST3D satisfy these requirements.

Conceptually, the spheres of inclusion/exclusion are composite geometric objects and search constraints.

The discussion thus far has illustrated the "mechanics" of defining parameters and limiting their values but these presuppose two very important decisions which have to be taken:

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Volume 1 Chapter 7 Choosing and Naming Geometric Parameters.