Volume 1 Chapter 6 Number of Fragments Instruction

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6.2.22 Implicit And Explicit Hydrogen Atoms

In all the examples illustrated earlier in this chapter each hydrogen atom has been terminal and its number has been specified as a property, nh, of the atom to which it is attached.

We refer to this handling as the implicit treatment of hydrogen atoms.

If you so wish, connectivity tests can be expressed in terms of explicit hydrogen atoms but this is not normally done since it involves the typing of more lines of atom property records.

Consider the search fragment: C-NH2

This can be formulated in the three ways (a)-(c) shown below:

(a) T1  *CONN       (b) T2  *CONN       (c) T3  *CONN
    AT1  C  1           AT1  C  1           AT1  C  1
    AT2  N  1  2  E     AT2  N  3  0  E     AT2  N  2  1  E
    BO  1  2            AT3  H  1           AT3  H  1
    END                 AT4  H  1           BO  1  2
    QUES  T1            BO  1  2            BO  2  3
                        BO  2  3            END
                        BO  2  4            QUES  T3
                        END
                        QUES  T2

(a)
This involves the normal implicit formulation with the N atom having nh=2.

(b)
This involves two explicit H atoms numbered as atoms 3 and 4. Note that the N atom now has nh=0 and each H atom has mca=1.

(c)
This involves one implicit H atom and one explicit H atom, numbered 3. In this case the N atom has mca=2 and nh=1; H3 has mca=1.

However, you must note that there are 3 situations in which explicit hydrogen atoms are used in the database:

6.2.23 Bond Type Conventions in the Database

In constructing a connectivity test it is useful to be aware of the principal conventions used in assigning bond types to structures.

However, you should bear in mind that if the search fragment contains several characteristic features, such as unusual elements and ring systems, then you might choose to ignore bond types by setting them to bond type 99, ie. any bond type. The disadvantages of this approach are that the search may run much more slowly and the number of unwanted hits may be unacceptably high.

A few of the more important conventions are listed below:

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Volume 1 Chapter 6 2D Searching in Graphics QUEST3D.