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

Select NO-LINKS

If NO-LINKS applies to the WHOLE fragment, select another command.
If it applies to TWO or more individual atoms, select each of these atoms.
(Select another command to complete NO-LINKS)

Select atom 4, then atom 7
The fragment is now as in (ii).
The symbol ----X---- at 4 and 7 indicates NO-LINKS at these atoms.

Select an atom for NO-LINKS (Re-select an atom to change your mind.)
(Select another command to complete NO-LINKS)

Select DEFINE-STRUCTURE

A search with this fragment would register hits for (iii) - (v), but not for (vi) or (vii).

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).

Select NO-LINKS

If NO-LINKS applies to the WHOLE fragment, select another command.
If it applies to TWO or more individual atoms, select each of these atoms.
(Select another command to complete NO-LINKS)

Select DEFINE-STRUCTURE

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.

Select NO-LINKS

If NO-LINKS applies to the WHOLE fragment, select another command.
If it applies to TWO or more individual atoms, select each of these atoms.
(Select another command to complete NO-LINKS)

Select atom 4, atom 5, atom 6, atom 7

The fragment is now as in (ii).

Select an atom for NO-LINKS (Re-select an atom to change your
mind.)
(Select another command to complete NO-LINKS)

Select DEFINE-STRUCTURE

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:

NO-LINKS cannot apply to only ONE atom. Please select at least one more atom,
or de-select the one you have already specified. Thank you.

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