Volume 2 Chapter 2 2D-Constrain Sub-menu NO-CYCLIC-ROUTES

Back to Table of Contents

NO-LINKS

Function

NO-LINKS is used to constrain the fragment such that:

either two or more specified atoms can not be linked directly to each other

or no atoms in the fragment can be linked directly to each other except by the bonds defined in the fragment.

Examples

Ex .1 Suppose we have built the fragment (i) - see below. Suppose we wish to constrain the fragment so that there is no direct link between atoms 4 and 7.

Note that in (iv) atom 4 is linked indirectly, through atom 9, to atom 7.

Ex. 2 Suppose we wish NO-LINKS to apply to the WHOLE fragment (i).

A search with this fragment would register hits for (iii) and (iv) but not (v) - (vii).

Ex. 3 Suppose we have built the fragment (i) - see below. Suppose we wish to constrain the structure so that there is no direct link between atoms 5 and 7.

If we placed no constraints on the fragment then a search would register hits for all of (iii) - (vi).

We wish to exclude (iv) from the hits.

If we simply specified NO-LINKS for atoms 5 and 7 in (i) then a search would still register a hit for (iv).

To obtain the desired result we must consider topological equivalence.

Thus, in (i)

atom 5 is equivalent to atom 6
atom 7 is equivalent to atom 4.

Therefore, all four atoms must be specified.

Note that this will also result in direct links between atoms 4 and 6 also being prohibited.

Now a search conducted with this fragment will register hits for (iii), (v), (vi).

Note that the procedure for changing NO-LINKS specification is analogous to that described for the NO-CYCLIC-ROUTES command.

Note also that if only one atom is specified for the NO-LINKS command then:

Back to Table of Contents

Volume 2 Chapter 2 2D-Constrain Sub-menu NOSCREENS.