Volume 2 Chapter 2 2D-Constrain Sub-menu GENERATE-HYDS

Function

GENERATE-HYDS is used to assign terminal hydrogen atoms to all carbon atoms in the fragment which do not already carry terminal hydrogen atoms.

If the valency of a carbon atom, as defined by the fragment, is less than 4 then this command will add hydrogen atoms so that the valency is raised to 4.

Example

Suppose we have built the fragment:

Select GENERATE-HYDS

The fragment is now:

Atoms marked with crosses either cannot have hydrogens automatically assigned,
or they have non-standard valencies.
Please use the HYDROGENS button for these atoms.

In the above example the N and O atoms are flagged in red. If we wished to assign H atoms to either of these then we would do so using the HYDROGENS command.

This command is often used when constructing an exact search structure to be submitted for an identity search or a similarity search.

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